The kokugo examples for sense 3 are archaic.
I don't think we need to explain what a ship is.

@@ -12 +12 @@
-<gloss>counter for ships (large boats)</gloss>
+<gloss>counter for ships</gloss>
@@ -20,2 +20,2 @@
-<misc>&rare;</misc>
-<gloss>counter for items carried in a bundle (fish, birds, arrows, etc.)</gloss>
+<misc>&arch;</misc>
+<gloss>counter for items carried in a bundle (e.g. fish, birds, arrows)</gloss>

https://en.wikipedia.org/wiki/Japanese_counter_word
せき seki	隻	Ships, half of a pair (e.g., half of a folding screen), item carried in a bundle (fish, birds, arrows etc.)

矢一隻	22	100.0%
矢二隻	0	0.0%
矢三隻	0	0.0%
My guess for counting arrows...
矢一本	384	75.0%
矢二本	38	7.4%
矢三本	36	7.0%
A fired arrow
矢一発	100

I didn't follow the implication of "etc." in [3].  Happened to find that wikipedia has an explanation, which seemed reasonable to me.  I see now this was also mentioned in 2012.  

sankoku has [1] and [2] (including the folding-screen example).  [1] is 船などの数を数える言葉. [3], missing in a modern dictionary, is probably [obs] or [arch] I imagine.

[1] is quite common.

@@ -20 +20,2 @@
-<gloss>counter for fish, birds, arrows, etc.</gloss>
+<misc>&rare;</misc>
+<gloss>counter for items carried in a bundle (fish, birds, arrows, etc.)</gloss>

daijr koj

* Add “half of a pair” sense
* Add fish, birds, arrows, etc.
* Clarify *large* boats
* Have fish, birds, etc. separate from ships, as per daijr – these feel like things you can carry in a bundle; I’m guessing this is *captured* fish, birds, as koj example suggests (carrying bundle of fish at waist) etc.
Saw at museum, referring to half of a folding screen (daijr mentions this usage).

@@ -12,1 +12,9 @@
-<gloss>counter for ships</gloss>
+<gloss>counter for ships (large boats)</gloss>
+</sense>
+<sense>
+<pos>&ctr;</pos>
+<gloss>counter for half of a pair (e.g. half of a folding screen)</gloss>
+</sense>
+<sense>
+<pos>&ctr;</pos>
+<gloss>counter for fish, birds, arrows, etc.</gloss>