I would assume that most ships have multiple reactors, as stated in SOM, and that the writers wrote that 10% and 50% thing as a simplification. The same way that mortgage is a simplification for what in real life would be way more complicated and involved. Interest, proper paperwork, insurance, bills of lading, bills of sale, what is involved in getting your ship declared spaceworthy, etc. It is not a simulation so much as an approximation.
Hell, We don't even know for sure if any of these rules apply to NPC ships or just to PC ships, because the entirety of the CRB is player-focused, not world-focused. As far as I can tell, no rules in the CRB actually apply to NPCs. The Trade section doesn't. Apparently, the character creation section doesn't, since I have been repeatedly told on here that NPCs do not use Careers. Shall I go on or are these examples sufficient?
If you are looking for exacting detail within the rules, then Traveller may not be the game for you. Those kinds of specifics just don't exist in Traveller. It is one of the reasons most of us have to write so many house rules or use whatever We can find from other editions.