If they jump in empty and you Hyper Bomb, they can jump out again. I’ve tried this many times and it never works on people who know what they’re doing.
However, if they jump in with an attack, you can Hyper Bomb through it if you time it properly. This is not always possible if the attack hits high.
I’m just trying to say that HB against an empty jump-in is not guaranteed. Sure you could get it to work if you know your opponent will try to throw you as he lands, but it is not like HBing someone out of a deep jump in where you could time it well and it will grab 100% of the time.
General rule for using HB is: if your opponent didn’t press a button before the super freeze, he can jump out. Unless he’s stunned, of course.