According to the rules any ship, base or other unit in excess of 30 Hull Spaces in size is required to have a Boat Bay and a cutter or larger small craft. I can find no place in the rules that stipulate a penalty or consequences for a unit that, for whatever reason, is lacking its required small craft. Is there any such information published?
For now our campaign's house rule is that a unit that lacks its required small craft operates at one crew grade less than normal. The idea being that a unit lacking its small craft for personnel transfers and routine special cargo handling has an efficency penalty. So if a unit loses its small craft, on the following month its effective crew grade drops by one but this penalty is immediately canceled as soon as the unit has a replacement small craft and can resume normal operations.