It depends on the server. I don't think there are many servers (if any) which actively encourage modding, but i'm sure there are some which won't mind too much if you just use a client-side visuals mod (eg trent's clothes or the custom civilian paint jobs). Some, however, (such as the ubiquitous Elite server) are quite strict on mods because they have been known to cause instability in the past. The best thing to do is check the rules of the server you want to play on, or mail the server admin.

oh, and by the way: all the gates are open right from the start in multiplayer.