Do you mean general multiplayer like Gamespy or IP connecting, and Orion Pirates?
Your files will not be altered. However, to play with others on Gamespy, you must be using Firesoul's OP+ 4.0 shiplist. It has to be installed over another mod (preferably from a clean OP installation), so in a sense it does interfere with your mods/shiplists: the ship and fighter lists have to be the same as the people you fly with. That's the only thing, though. Models, graphics, and sounds are left alone in multiplayer.