To "scan" deep space, you simply travel to that system. If a hidden system is there, it will appear on your screen when you arrive like any other system does. Otherwise, it will appear as a deep space coordinate.
Black holes only appear in systems - it's not even possible to put them in deep space. So if the coordinates you're scanning are not a system, you don't have anything to worry about. If you arrive in a hidden system, it is possible (but highly unlikely) that the system will contain a black hole. This won't appear on scanners, but in the system travel page you may notice a very large gravity well where there shouldn't be, based on the planets in the system.
Black holes are largely a non-issue, because they can't pull you out of hyperspace and can usually be avoided by being smart if you notice a weird gravity well in the system.