"I'm not gonna use the names of the actual drugs, but one makes you a tweaker, and one makes you a heroin addict." I find that line both unintentionally funny and incredibly horrifying.
Well the guy who plays the T-1000 is cut, and you can kinda see his wang in the scene where he squats down. There was a company hired to digitally remove his giblets from that scene, they didn't do a very good job.
The T-1000 would go with whatever it either knows or guesses its target is packing, that includes cut/uncut, as well as other details like body scars, tattoos etc. Otherwise it might stand out if it had to use a public shower etc and it was the only uncut dude in, say, America.
I reckon it could get rumbled if you were a resistance fighter, and knew your buddy had a tattoo, say, on his shoulder, and the T-1000 didn't simulate it because it didn't know it was there. But the T-1000 seems like it doesn't like spending lots of time trying to infiltrate, it moves on, slips through defenses by looking like it belongs there and swaps forms often so people don't realize someone's slowly getting closer and closer to the protected core of their base, since it just looks like Suzy's walking back to her office for something, then the janitor just has to double back to get his mop etc.
I still reckon for deeper infiltration something like a T-1000 would probably strip its target after it killed them, and make sure it's got every tattoo, every scar, every wrinkle absolutely perfect. In lieu of that information it'd do a best guess based on age, general physique etc.
For the earlier flesh models, Skynet would pick whatever it thought was most likely. I'd imagine it'd do the process surgically, so the circumcision scar looks normal.
This has actually come up before, and people derided Skynet paying attention to small details like genitalia as "silly", but let's be real, if you knew the robot couldn't simulate junk properly, you could probably do a quick anti-Terminator test involving dropping trou. If sports players/soldiers can get used to it for efficient hygiene, resistance fighters would get used to it as a legit security measure.