i think when the aeroshuttle leaves, a hatch pushes down from above, it looks just like the aeroshuttle so a potential enemy wouldn't know it was gone just by looking at the ship.![]()
But when the aeroshuttle is docked, you then have to explain where that hatch stows into and whether it's just unused cargo space, or making a rec lounge temporarily unavailable.
If a hostile's sensors are sophisticated to enough to see that a shuttle is missing from the berths, then they're going to know the aeroshuttle is gone too.