Assuming that the front of the TOS starship nacelles contained the matter-antimatter reactors (those of the Constellation had been destroyed), there'd be indeed little reason to keep antimatter supplies in the warp nacelles as these would only constitute an unnecessary hazard. Could be a useful hint that the Constellation belonged to the Constitution Starship Class (NCC-16XX) and only the Enterprise Starship Class (NCC-17XX) featured another M/AM reactor in the engineering hull and the antimatter pods on Deck 11. I most certainly don't. The amount of energy you need to put into the creation of antimatter equals the amount of energy yield you could get from matter-antimatter annihilation ("You canna change the laws of physics"). These enigmatic antimatter generators look like "magic". On the other hand, if those large deuterium tanks (e.g. NCC-1701-D) were antimatter tanks I believe it might be easier to rationalize that space energy and/or matter is collected during flight. Hydrogen particles are available in open space, antimatter is not. I would find it much easier to assume that warping space requires less M/AM annihilation than assumed. However, matter and antimatter tanks should have a more or less equal volume to credibly illustrate the 1:1 annihilation ratio. Bob
That's a possibility. Of course warp drive and dilithium crystals look like "magic" as well. The amount of power the TOS Enterprise puts out is quite large (push a moon, go for it!) and her range is so great (Andromeda galaxy, no problem with fuel ) that she has effectively an unlimited, regenerating supply of antimatter. How she regenerates antimatter that's the magic. We've discussed this before in other threads whether it's dilithium tapping into an alternate antimatter universe, a variation of the zero point energy, etc. It just "works". I don't think she carries giant fuel containers but large enough tanks to power her for a while under full load and to look like a nova when it goes off catastrophically. TNG's tech went in a different direction (which I'd argue it's a different tech in a parallel universe) where their science and technology wasn't as magical. They did have fuel limitations with their warp drive although they slipped back into TOS thinking in "Booby Trap" where they burned more m-am fuel in a different dilithium arrangement to extend their am fuel supplies...
One other thing I forgot to mention is the different thinking of the TOS writers. Back then, they depicted antimatter as something more powerful than what we know today. Such as an ounce blasting half an atmosphere away and affecting a ship 30,000 km distant in "Obsession" or a small quantity enough to blast apart an Earth-sized space amoeba from the inside as in "The Immunity Syndrome". So I don't think in TOS there would be a way to inert the fuel. Jettison the pods containing the fuel, yes. Terminology-wise, in "The Apple" they were specific that potency was being lost in the "antimatter pods" and these pods were mentioned to be ejectable whereas "The Doomsday Machine" they say specifically "the antimatter" which is much harder to assume that they meant "the antimatter fuel system" instead of the fuel itself. There just isn't enough context to go further than the fuel, IMHO. Tangentially, in TNG, antimatter was made more-or-less harmless as evidenced by the antimatter show distraction in "Best of Both Worlds". It could destroy ships, but you'd need a whole lot more to do it.
I feel the need to rethink the opening in my last post. Again, the original dialogue: "Somehow the antimatter in the warp drive pods has been deactivated." Washburn's report clearly suggests that the assumed shut-down of the warp nacelles' M/AM reactors and the venting of antimatter supplies was "somehow" initiated by the planet killer. We all remember the scene where the planet killer apparently wants to suck the Enterprise inside (to risk it blowing up?!?) which may be a misinterpretation of what would have actually happened in the next scene: A beam from the maw of the planet killer, disrupting the M/AM reactors at the front of the nacelles, thus initiating an emergency venting of antimatter which the planet killer then takes in to replenish its own antimatter ("anti-proton") supplies... What a clever way of the planet killer to disable an attacking ship: by stealing its source of power and - worse - adding it to its own power supplies. I'm more and more inclined to believe that matter-antimatter annihilation and dilithium crystals are somewhat combined to enable the ship to tap into the enigmatic (but "real") dark energy which is the actual element that enables the warping of space (unless I'm mistaken that's the only property of dark energy that has been observed, it warps space). It never ceases to amaze me, that this idea apparently had already been brought forward to Franz Joseph Schnaubelt in 1976: "But in theory you would need only a very, very tiny antimatter-starting chamber to start the whole mechanism pulling in energy. Dilithium crystals are very unstable, so with a starting chamber full of dilithium, a few added atoms of antimatter will provide the driving force to get the whole system charged up and sucking in space energy. Now beyond that..." Bob