In the DATA/UNIVERSE/SYSTEM/<system> folder you'll find an INI in each respective directory. I've been trying without success to get the New Berlin -> Sigma 13 jumphole working in MP, but here's what I've found so far:
The file I'm working with is <above dir structure>/RH01/rh01.ini. If you scroll down to the bottom you'll see a section that looks like this:
[Object
nickname = Rh01_to_Bw05_hole
ids_name = 260721
pos = 28710, 0, 21099
rotate = 0, -155, 0
Archetype = jumphole
msg_id_prefix = gcs_refer_system_Bw05
ids_info = 60212
jump_effect = jump_effect_hole
visit = 128
goto = Bw05, Bw05_to_Rh01_hole, gate_tunnel_bretonia
If you change the "visit = 128" to "visit = 0" then the jumphole will at least show up on your map with the right label, however I still get "Access Denied" when trying to dock with it. I've tried changing the ids with no success (that just changed to a different jumphole which STILL said "Access Denied" and commenting out the subsequent [zone sections beneath that [object.
If anyone has any more info on how to activate the jumpgates in MP, please let me know!
Oh, and commenting out the locked gates in the initialworld.ini doesn't really seem to help, though I did it anyway. Pretty sure that only affects single player.