In "The Apple" Scotty refers to the antimatter pods being inert and in reply to this, Kirk tells him to jettison the nacelles if possible; so at the very least, the pods are in the nacelles, but more likely they are the nacelles.
Umm, why jettison inert antimatter pods?
From "The Apple":
KIRK: Then use your imagination. Tie every ounce of power the ship has into the impulse engines. Discard the warp drive nacelles if you have to, and crack out of there with the main section, but get that ship out of there!
I think in that context, Kirk saw that the ship needed to escape and they were short on power to do it. If they discarded the nacelles which contained the inert antimatter pods, then that would lighten the ship.
From "Errand of Mercy":
KIRK: All hands, maintain general alert. Hold battle stations. Damage report, Mister Spock.
SPOCK: Minor, Captain. We were most fortunate. Blast damage in decks ten and eleven, minor buckling in the antimatter pods, casualties very light.
Or Spock could be just listing separate items since he doesn't directly connect them by saying: "Blast damage in decks ten and eleven resulting
in minor buckling in the antimatter pods and light casualties."