All that happens with the hanger being vertical is that the ships fly in rotated at about 45 degress to the plane of the hanger. The approach lights are lined up fine, its just the flight of the ship thats wrong. You'll probably not even notice for AI ships, just if you fly in yourself.
You know when you are docking with a factory and the autopilot doesn't fly in flat but rather rotated to the plane of the approach lights? As you reach the dock at the last minute the AI levels out the roll and lines up. Well in this case, it doesn't do those final adjustments and just continues in at an angle.
The vertical launch tubes are fine, its just the hanger.
I did wonder why none of the vanilla ships have vertical hangers - now I know!
Oh - and there's no risk of collisions while docking as collision detection is disabled for docking anyway - this is the case with all types of docks in vanilla.
As for sending the ships over - its entirely up to you. The hanger issue doesn't bother me too much. Just be prepared for loads of people moaning that their ships fly in at weird angles!
