iSuck: that depends

the engine does load pk3 files installed in pathto/Nexuiz/data AND in ~/.nexuiz/data the first one would be for all users that play Nexuiz, the second just for the current user.
If you were a admin that wants his users to play the first would be appropriate, if you are 'a normal user' it does not matter. however if you are the only user and use several Nexuiz installations (like to test the hotfix or just for the fun of having 2.3 and 2.4 installed or whatever) the second path will kinda share those maps among all your Nexuiz installs.
Hope that makes it clearer?