it matters a lot if you're doing things to ROMs or playing them via a backup unit, but if you're playing in an emulator it doesn't matter at all - with most emulators.
Yah, I already use Tool64 to convert them. But I've noticed that whenever I load a ROM, PJ64 spends about half a second byteswapping it. Plus there's that odd bug with uHLE. So I'll prly convert them all to v64.