moritz already demonstrated how precedence might break.

Further, context might break. (Update: And tye said so already, while I was writing this. Eh.)

Given those prototypes, files_identical( foo(), bar() ) currently means files_identical( scalar(foo()), scalar(bar()) ). Dropping prototypes means putting foo() and bar() in list context instead.

If foo() is (or returns something that is) context sensitive, this may break.

(Likewise, inspection_current( @array ) will, given the prototype, get the number of elements in @array. Without the prototype, it will get the first element. Given that this argument is called $file, this is a rather far-fetched scenario, but should serve to illustrate context sensitivity.)

In this case, the standard wisdom on prototypes may well be trumped by the standard wisdom of legacy code:

If it ain't broke, don't fix it.