I imagine any network does their own cuts.
It's not Trek, but I find it annoying how childishly Hallmark channel cuts shows like "Fraiser" and "Golden Girls" (guilty pleasure on the last one; so sue me!)
They are constantly bleeping out (well, muting) the most low-key of "profanity" - words like "crap" and "ass" and "hell" and "damn" - simple stuff you can hear at 8 pm. Even if the rerun is airing at 11pm or 2 am, it'll still be muted if someone says anything above "heck" - and I find that really lame and silly. Especially when you're talking a show like "Golden Girls" or something, lol.
As far as time cuts and Trek... I imagine it's individual networks that decide how/where. I know BBCAmerica cuts TNG for time.
I wish we had a law or something against such. Something about preserving the artists original intent. :P I hate to see anything cut, especially by hacks and for time and content. I can't watch a movie on anything but pay cable or DVD. If it's on basic cable or broadcast, it's just been cut to shit by the moral crusaders and the advertising bean counters.