[Ydiss]

I'm almost 100% certain that keeping your pk3 map files in your main folder will not slow your performance, as all of your map files are kept there, even the original stock ones (Algiers, Crossroads, etc).

Map files (or bsp files) are only read at the initiation of the level. The only part of a map file cluster that is read during play is the script file and this won't slow play down whatsoever.