So far T2 took down only the most popular total conversions and the reverse engineering project, the regular stuff (model, scripts, etc) are still there. Actually, what they did was an half-assed job, because you can still find mirrors of those "deleted" mods.
IIRC they also unofficialy halted the lawsuit against the authors of re3/reVC, according to a GTAForums post.
While I totally agree that taking down mods is a scum thing to do, I must admit that most users of GTAForums had a massive spergout due to it. According to them it seemed like they nuked every mod existing to this point, while in reality they just took down the hottest mods and then stopped. Looks like their legal department is sloppy as their development one.
EDIT: While I'm at it, I also want to point out that there were more mods taken down by the authors themselves rather than Take-Two. Looks like the scaremongering did more damage than the DMCA itself.