Why remove them? Are they causing problems? If it ain't broke don't fix it

Perl prototypes are not like C/C++ prototypes (which many programmers do not understand anyhow) they force the context. Their strength is in detecting errors at compile-time, which is particularly useful when passing references to specific types, like arrays and hashes. Sure, you can check the correct type has been passed using ref, but at best you can only generate a run-time exception in this way.
Their weaknesses are that they are ignored by OO programs, and by most people, since they are optional. This means that their subtlties are not generally understood, life's too short.