Depends on what you mean by 'through'. If you mean just flying past in hyper, it won't pull you out of hyper. If you mean travel from one side to the other, sure, but why would you want to? There are blackholes dotted around but quite hard to work out where they are.
I need to fly through to get an abandoned ship, but like you said it is tough to figure out where the black holes are because almost the whole area is a gravity well
Yeah, I planned it that way while I was building it. Best to enter the system from the side closest to where the ship is, otherwise you risk running into blackholes between them.
No black holes will not pull you out of hyper .... just when you are navigating at the sub light speeds you cannot see them so your chances are pretty good you will hit one. And yeah if you hit one it is big bowl of Carnations Insta-Death
Well there was plenty of warning about the change - I told people that there would be new blackhole systems around, including the galactic center, as well as the system being on dev months before it went live on main.