odin: Exactly, the Mods need to be recompiled (for Q3 if I remember right it's again download and run).
So it's like for Heretic II for Quake 2 (well, same engine).
In the meanwhile there are 61 Mods ported to AmigaOS, which of course does include nearly all important Mods.
You can run server-side Mods even when no ports exist (if the Server is a PC), but most Quake 2 Mods being played (with some popular
Server-side Mods being the exception) are not only Server-side and need to be ported. Mods like (all already ported) ChaosDM, ActionQuake, The Weapons Factory, Battle of the Sexes, StarTrek Quake 2, Star Wars Quake 2, Headhunters, Gloom.
Steffen