The filename conventions post that PencilVoid linked to covers it, but the general advantage of the filename prefixes is to make the files easy to search for when sorted alphabetically, and help provide an indication of what each file is when just viewed in your SRB2 folder.
This generally comes in handy when you're trying to find an old file you haven't used in a while, or you are sorting through your folder of netgame downloads and you're not sure what file does what because you got them all at once through a netgame download and not from the message board.
We actually dropped V as a required prefix not long ago though, V stood for Vanilla (to differentiate them from the K for Kart files) but with the staff changes and the opportunity to take another look through the rules it was decided that V was redundant. It's just not a big enough deal to punish someone and put them back in submissions until they change the filename now, that would be much more trouble than it's worth.