I'm very new to SWC, and I'm a little concerned about black holes. From what I read you can't see them on the map --- is this still true as of now? If so, how can I be sure to avoid them?

There are select systems where blackholes appear, to be seen on the galaxymap.
Best to avoid those systems if you have no reason to visit them.

Is there a list of systems with black holes in them? Or any warning sign that I'd be going to a system that contains one?

Black holes show up on the galaxy map, but not their locations. For example, http://www.swcombine.com/rules/?Galaxy_Map&systemID=1465 contains black holes.

You can infer their locations from the grav well view.
Your ship will automatically route around black holes when travelling in sublight, which can reveal their locations.

Yeah, if I'm correct there will be a red overlay "patch" (for lack of a better word) that represents a gravity well, like around planets and suns, on the sublight screen travel screen. There just won't be anything visible at the center.

As Clarr said, your ship will automatically route around them in sublight. As long as you don't specifically travel to their location (meaning, you only travel to a sublight square containing a planet or space station) you'll know that you're perfectly safe.