I believe that the clock runs in commercial hangars though.
Maintenance clock does, but deployment clock does not. In fact it winds back, probably the same as with a military hangar.
You could stick a station with a military hangar inside a station with a commercial hangar. Ships docked with the military hanger will rewind their maintenance clock and their deployment clock. However the military hangar station itself will tick up it's maintenance clock when docked in the commercial hangar station.
The solution is easy, dock the commercial station into a bigger station with military hangars - I would call it the babushka class hangar carrier/tender
That works too but I am not sure you gain much by having a smaller dedicated military hanger within another military hangar. There would also be other design trade offs since now you would have a larger military ship rather than larger commercial ship.
The thing I like about the larger commercial ships is that they have no MSP upkeep.
That said, if spoilers are already in-system, MSP upkeep is probably a lesser concern than survival.
