Well that is a good point. I suppose it would depend on your rank/position for the campaign. It would be unlikely that you would miss out on any missions if you were a flight lead or squadron CO but if you where the low man on the totem pole you could get bumped from the flight. I would think that as a flight lead or squadron CO it could affect you by being short on aircraft for the next mission. All of that would of course depend on OP tempo, # of A/C required for each mission etc.
As an aviation officer I know what sort of operational effects over torquing an aircraft can have on your maintenance flow and consequently your operations. I do understand, however, that this is a flight sim and not a maintenance sim so it would definitely not be everyone's cup of tea. I do think it could add a new dimension and some realism to the sim as being 4/4 or 8/8 on aircraft for all missions all the time is a but unrealistic especially when factoring in maintenance and combat losses. Perhaps it could be a toggle-able option and decisions regarding planes/pilots for each mission would depend on position and rank.