Antimatter "deactivation" -- powerful subspace fields disrupt the antimatter containment of approaching ships. ... Anyway, "deactivated" refers to a safety shutdown of the antimatter plant and venting of the day-bins. This also neatly explains the no torpedo bit... No antimatter, no torpedoes.
Welcome to the BBS! Shall we take another look at the original dialogue?
WASHBURN: ... Somehow the antimatter in the warp drive pods has been deactivated.
KIRK: Deactivated? Scotty, could some kind of general energy dampening field do that, and would the same type of thing account for the heavy subspace interference?
SCOTT: Aye, that all adds up. But what sort of a thing could do all that?
I'd agree that "deactivating" is a rather confusing choice of words, but the context suggested that the antimatter had been rendered useless, not
its magnetic containment, IMHO.
(and the antimatter aboard the Constellation
hadn't been vented, otherwise Washburn would have probably reported that)