There would be no reason to dump the nacelles if they weren't the matter-antimatter generators.
Oh, dunno about that. They are so much dead weight if they are out of commission, after all. In "The Apple", the reference to cutting them loose is combined with the idea of paring down the ship to the essentials in other ways as well, so that the impulse engines have a better chance of saving the "main section".
other reference to nacelle jettison, from "The Savage Curtain", may indeed be related to the nacelles being volatile. But "That Which Survives" shows that a singular pod somewhere in the bowels of the ship is the bit to be ejected when antimatter fuel flow cannot be otherwise controlled; "jettison" might refer to antimatter pod jettison in both cases, rather than to the already disengaged warp nacelles.
As for the rest of the "pod" references, none of them indicates an outboard pod explicitly. All could thus tie together (a definite plus in jargon) and refer to the indoors, user-accessible antimatter storage pods of, say, "That Which Survives" fame. In that sense, all of these references support an internal storage arrangement for antimatter.