Yes, you'll see these not infrequently. I believe that the info shown for the installation or guarded area includes ownership/faction info. If you were to do something to skimmers, etc, that's who'd you'd likely end up getting a fine from. Even a logged trespass is just a fine, not a bounty.
Dangerous is a ranking. You could shoot/destroy them without much consequence if they're marked as wanted. You would actually get a small bounty reward, iirc. 1,000cr sounds familiar. In that case, I don't ever remember running into any trouble when destroying them.
The context for me doing that was mostly because I found occupied escape pods or other cartridges of goodies in their little area. You can pretty easily just swipe objects that you're interested in without even destroying the skimmers. They don't attack instantly when you breach the perimeter. They're also not very smart and will continue to patrol the (now) empty area if you relieve them of their stuff!