Out of curiosity, will the ships power just be the power of the mother ship? Or will it be a combination of the Mother Ship and the ship(s) that is in it's hanger?
That's a good question. The ship power itself will remain the same, but I think if you get a "Com" mission with the mothership will several other ships in the hangar bay, that all ships in hangar plus the mothership should count toward the mission rating / power you get (or at least some of the power of the ships in hangar bay, maybe 50%).
For the record, I refer to a mothership as a ship carrying other ships in it's hangar bay / belly, it can be any ship, it doesn't need the mothership optimization to have a hangar bay.
The mothership optimization will add +75% Hangar bay, +75% Cargo bay, -25% Navigation time
The hangar bay doesn't affect the mothership in any way regarding power levels.
The power rating of a mothership entering combat is not affected by the ships in it's hangar bay.
If a ship undocks from the hangar bay, then it is added to the attack / power rating calculation, if it's the hangar bay it will not participate in combat.