The Reactor Factor

Im of the opinion that all ships should have a reactor on board. Chem rockets are not getting the power from the engines. I'm having difficulty seeing how Ion engines supply a ship with power and the "atomic" drive sure, but if its atomic drive, which make great targets sitting out there away from the hull are shot off or some other catastrophe then what? Most civilian ships can get by with a size A fission reactor but military ships require at least one reactor equal in size to the engines its using just for dedicated power source for weapons and shields