Hickory: It's not just the amount of files that can cause slowdowns. Badly written mods, especially script-heavy mods, can do far more harm in this respect than file numbers.
Ergos: That's why I said "usually". In this case, we cannot be sure that the culprit is a mod, and uninstalling mods mid-game can severely mess your game. So, unless ousteroune wants to start again from Irenicus dungeon, I would wait and try something else first.
Uninstalling mods should be done only as last resort, and even so, I would make first a copy of the bg2 folder and work on the copy by uninstalling mods one at the time to identify the one(s) responsible (if any).
Right, and ousteroune's game is not already messed up? Of course it is, that's why he/she has posted this question. Uninstalling mods, when so many are installed, is the
only sensible thing to do at this stage. Did you actually see the weidu log? Uninstalling mods is absolutely NOT a last resort.