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.
There is no reason you can't do this but my suggestion would be to not do so unless you notice the players abusing this. Especially as asault shuttles are entering service the utility of them will become obvious but also the tendancy for the odd one to be lost in combat. So long as the player doesn't ignore that, and works to replace the losses there is no real need to impose a penalty. If on the other hand they don't replace them on some sort of reasonable time frame I would then do something. But it is one thing that can be easily forgotten especially when doing things like pre-fab assembly. I've gotten better about remembering to build small craft and ship them out with the pre-fab parts but I still sometimes forget.