ふうふう言いながら	4249
フーフー言いながら	4075
フウフウ言いながら	1097
フゥフゥ言いながら	540

It's true that raw n-gram counts don't always give the full picture which is why it can be helpful to add some context to the search terms.
フウフウ and フゥフゥ are irregular but not exactly obscure. I think they're worth having.

I considered adding ik tags but with these sorts of on-mim terms it's usually difficult to 
do a regular/irregular division. I'll tag them now. The reason I like including forms such 
as フウフウ is that I want someone encountering them to be able to look it up. I wouldn't 
bother if it was quite rare, but in this case it's not.
As to whether フウフウ et al. have this meaning, well I assume Rene checked when he added 
them.

@@ -14,0 +15 @@
+<re_inf>&ik;</re_inf>
@@ -17,0 +19 @@
+<re_inf>&ik;</re_inf>

You have to look at the actual usage of things like フゥフゥ too. You can't just always lean on those n-grams.
And if you keep them, they should be tagged as incorrect.

Google n-grams:
ふうふう	35339
ふーふー	34057
フーフー	52594
フウフウ	6079
フゥフゥ	4137

Enough use to be worth keeping.

@@ -3,0 +4,3 @@
+<r_ele>
+<reb>フーフー</reb>
+</r_ele>
@@ -11 +14,4 @@
-<reb>フーフー</reb>
+<reb>フウフウ</reb>
+</r_ele>
+<r_ele>
+<reb>フゥフゥ</reb>

I don't think フゥフゥ and フウフウ are necessary to include in this entry. Both are "incorrect" orthographically, which would be fine 
according to the dictionary style if they were at least common, but they don't seem to be. The first hit on Google for フゥフゥ is this 
entry. For "フウフウ" I just get ふうふう.

@@ -12,6 +11,0 @@
-</r_ele>
-<r_ele>
-<reb>フウフウ</reb>
-</r_ele>
-<r_ele>
-<reb>フゥフゥ</reb>