I guess we can close this now.

＞ The usage is the same: they are all semantically equivalent - they negate; and also syntactically equivalent [...]
   ＞ Yes, I wasn't very clear on the fact that I was talking about the "character", i.e. connotation.

After mulling this over for a bit, I think I'll drop it. It's most likely easier for everyone involved if we stick with your superset approach.
I was attempting to extract a "general connotation" from the references, that being "文章的".

"So, do we describe it according to its use in dialects which have the sheer numbers, or according to the standard tongue which bears the heavier weight and is the most sought after?"
＞ this does hit the nail on its head, yes. It's really both or neither.


In any case, thanks for the discussion.
This is it from my side then

Ironically, the first three references exhibit exactly what I was talking of: Daijiring speaks of its aged and literary disposition, Shinsen highlights its use in dialects while Sankoku says it sounds theatrical - three quite different descriptions, and none of them wrong.

"I think it can be said that usage of ない and usage of ぬ・ん (and their respective connotations), in standard Japanese, are different."
The usage is the same: they are all semantically equivalent - they negate; and also syntactically equivalent in terms of their distribution against verbs with the one exception of the great サ変未然形 incident of 99.
I do realise your concern is elsewhere, but more on that later.

"A learner that encounters ぬ・ん and happens to see this entry may surmise that he can just use ぬ in ない's stead, since they would both be unmarked entries."
Well, they can. The interlocutor *will* wonder what kind of wacky textbook they have been learning from; but due to the above-mentioned equivalences, they will be fully understood and produce a completely grammatical sentence.
Besides, a learner is unlikely to actively use ぬ・ん as they will be coerced into using ない both by the fact that they are likely already being taught to do so by whatever material they are using beyond this dictionary, and by stimulus from actual standard Japanese. I personally think this is of least concern.

"Furthermore, I believe that the widespread dialectal usage of ん instead of ない cannot be as easily dismissed, as it spans large parts of the country."
I understand your position: we can neither apply every tag at once nor write a colossal note explaining every detail - but surely we can list that which is most common and/or important.
Normally I would heartily agree with that, the obstacle is that in this case none of the many flavours ぬs or んs are particularly uncommon or rare to find (except maybe informal/colloquial ぬ).
A very good example is precisely the dialectal ん: in absolute numbers, I would wager it might be the most numerous instance of ん... but I would also wager that it is not the most prevalent ん within the limits of standard Japanese, even when you disregard ません.
So, do we describe it according to its use in dialects which have the sheer numbers, or according to the standard tongue which bears the heavier weight and is the most sought after?
One could make an argument for either or both - I am opting for neither.

This situation can be spoken of in analogy to the many groups personal pronouns: e.g. わたし、おれ、ぼく and わたくし all intersect in being first person pronouns - at their core function - but each undeniably attributes a very distinct personality to the referent and/or atmosphere of the context in which they are employed.
This is the same with ぬ・ん, and constitutes the differences from ない that you spoke of previously - not in function or meaning, but in "character".
That as it may be, where ぬ and ん differ from the pronouns is that while the connotations of each pronoun are largely cast in stone according to the word itself, the exact character attributed to the speaker (and/or atmosphere) by ぬ・ん is not so, and varies wildly according to the setting.

Since we can neither predict what setting they will be encountered in (and thus the "variant" the reader is looking at) and nor can we easily overcome the throes of weighing what should be indicated and what is to be omitted, I say: the negatives ぬ・ん are the superset which includes the archaic negatives ぬ・ん, the dialectal negatives ぬ・ん, the frozen (in set expressions) negatives ぬ・ん... et cetera; so we might as well just go with one-size-fits-all.

If it seems I skipped anything, it is because the previous draft of this response was roughly twice the size and something had to go.

ぬ
Daijirin's footnote as well: 「ぬ」はやや古風な言い方や書き言葉的なものに用いられる。
Shinsen: 口語では、「ない」が一般的。「ぬ（ん）」は方言でも使われる。
Sankoku: 「信じられぬ！」のように、話しことばで使うと、芝居(しばい)がかった重々しい感じが出る。
Oukoku: 主として文章語の打ち消しに用いられる
Daijisen: 打消しの助動詞は、共通語においては「ない」を用いるのが普通で、「ます」に続く「ん」以外の「ぬ（ん）」は、主に文語的表現や慣用句的表現に使われるだけであるが、関西を中心とする西部の方言では「ぬ（ん）」が広く用いられる。連用形「ん」は「んで」「んでも」の形で用いられる。
Nikkoku: [...]現代の書きことば的また慣用的な表現に使われているもの。現代の話しことばでは、「ません」の場合を除いて打消にはふつう「ない」が用いられる。ただし、本州中部以西では話しことばでも「ぬ」を使うことが多い。
(The last part of nikkoku's note describes what is depicted in the map down below.

.

Firstly, I realize that "colloquial in standard Japanese" for ん is not very helpful since ません is where a learner will most likely first encounter ん, that not being colloquial usage at all. Hence me just suggesting it rather than editing the entry.

I also do not believe that there is a certain stiffly defined difference, that is rarely the case.
Without getting into all the context examples you have listed, which are reasonable but beyond the scope of a simple dictionary entry, I think it can be said that usage of ない and usage of ぬ・ん (and their respective connotations), in standard Japanese, are different. Multiple references outline this fact in their notes for ぬ. 
A learner that encounters ぬ・ん and happens to see this entry may surmise that he can just use ぬ in ない's stead, since they would both be unmarked entries.
I think it can also be said that ん is at least in some respect a "lesser" form of ぬ, as it usually the case with contracted or abbreviated forms (apart from ません). 


Furthermore, I believe that the widespread dialectal usage of ん instead of ない cannot be as easily dismissed, as it spans large parts of the country.
I certainly do not wish to make that fact the focal point of this entry, but in my eyes it would be somewhat disingenious to completely disregard it if we already include ん.
Thus I would personally like for this entry to, in one way or another, include information regarding the やや古風・文章的 aspect (especially of ぬ), and the dialectal aspect of ん specifically.
As per the visible dichotomy of ない・ん in the 方言地図 on 否定助動詞, in which ぬ plays a rather marginal role.
This being the main reason I proposed a separate sense for ん.

Perhaps this could be done by having the first sense unrestricted and the second like in my proposal down below, this is obviously contingent on the way my ideas are received in general.

Daijirin's entry for ん is in fact just a brief redirect to the entry on ぬ: 「（助動）〔打ち消しの助動詞「ぬ」の転〕」
And ぬ's entry in question lists its paradigm as: 「（助動）○・ず・ぬ（ん）・ぬ（ん）・ね・○」
Also, the relevant footnotes: 「「ぬ」の終止形・連体形は話し言葉では「ん」の形で用いられることが多い。特に助動詞「ます」に付くときは、「ません」のように「ん」の形が一般に用いられる。」

They are interchangeable in practice and I personally do not think it worthwhile to distinguish ぬ from ん; I find the differences in between them are not sufficient or consistent enough to warrant another sense - it is purely a matter of style and is not so stiffly defined; with the exception of ぬ never really being just colloquial (at least as far as I know, maybe there is a dialect somewhere), whether ぬ or ん are seen as formal, colloquial, dated or even as archaisms depends heavily on the context in which they are encountered: Old-fashioned literature pulling out all the old conjugations and auxiliaries? Archaisms. Co-occurs with an honorific? Formal or both formal and dated (ません vs ませぬ). Taking a stroll over the 近畿 region? Colloquial. Grandpa uses it and nobody else does? Dated colloquial... etc.