I am not sure, as I don't (yet!) play on the server, but it may have to do with HDD space. When you add the Nether, it adds about 1/2 of the space of the normal world. For example, if you have four worlds that you play in, that will equal an additional two for the Nether, in HDD space. Also, if you have players in both world, it is having to do multiple more times loading/unloading chunks, since the players are going to be more spread out. In the end, if you have a moderately to highly populated server, it can be best to turn off the Nether!