I think I may have a solution to the hyperspace capable squadrons conundrum:
Create a host for them that is tiny and invisible. It would be unseen and not capable of being attacked. This way it could hyperspace in and launch it's squadron (not so different from the squadron emerging from hyperspace directly).
Now the difficulty is in how to control the fighters - especially when it comes to telling them to hyperspace out. One potential option is to tie the squadron's target to the target of the host (don't know if this is possible or not). Give the invisible host the squadron icon and issue it orders and the squadron acquires the target as well. The invisible host would be very fast and stay with its squadron so that the icon remains in the appropriate place.
Another potential option is to utilize the fleet mechanic to allow you to select the squadron by selecting the invisible host thus issuing them attack and move orders indirectly similarly to the first option. Not sure if it is possible to have squadrons join fleets with their host automatically though.
Last (and least desirable) option is to forget trying to abstract it and just admit that there is an invisible host ship that you have to issue your orders to while issuing attack orders to its squadron.
Now we are presented with the problem of destroying the squadron if the invisible host is invulnerable (and invisible). As a solution, firstly the host's fighter building rate could be very slow (maybe 1 fighter in 5 minutes or so). This is to stay true to the idea that its squadron is an autonomous unit operating independently and to prevent you from having a never ending squadron that you can't kill or chase off. Then maybe it will be possible to set it to self destruct when its squadron reaches 0%. Or if this isn't possible, remove its invulnerability when its squadron reaches 0% (in that case maybe instead of making it invisible give it a fighter mesh so that it can be killed when the time comes), don't know if this is possible either.
I know there were a lot of maybes in there but hopefully one of those methods is possible with the Sins engine. And if not, oh well, I tried