[TurboFool]

As rainfreak intimated, installing programs to your memory card is generally a good rule of thumb to avoid. Some programs don't function properly when installed to a memory card, some programs cause boot loops when installed that way, and when you accidentally eject your card while your phone's running it can get really messy.

That said, obviously since your memory card is not the ROM, when you flash the ROM it has no clue what's on your memory card and won't touch it, so you would need to delete those folders to clear them off. If you reinstall an application to it later, it'll overwrite any standard files, but if there's random temp files or other things created on the fly, those may remain.