I think it is pretty clear from this and TMOST that the fuel for the main engines is stored in the engineering hull, not in the nacelles. I see the nacelles as only serving to produce the warp field that propels the ship, not the power for the rest of the ship's systems.
Except
The Making of Star Trek explicitly says otherwise. I'm glad you brought up TMoST, so we can add in what it says as well.
From page 191:
The two long nacelles, atop the ship and attached to the engineering hull by slender pylons, house the main starship engines. The engines are each 504 feet long, 60 feet in diameter, operate via controlled fusion of matter and anti-matter, creating the fantastic power required to run the Enterprise and drive it at faster-than-light speeds.
I mean, it could hardly be clearer. The matter/antimatter reaction occurs in the engines that are housed inside the nacelles to create the fantastic power that drives the ship.
Granted, it's not a Roddenberry quote IN ALL CAPS, but it's as good as it gets in TMoST.
So, according to that episode, the matter/anti-matter reaction takes place in the engineering hull.
Really? What is the line of dialog that says this? Let's activate Chrissie's transcripts now and see what dialog we have to work with.
http://www.chakoteya.net/StarTrek/69.htm
So, first of all I searched for the word "hull". Zero hits.
Next, "engine". (That also gets "engineer", "engineering", etc.) 17 hits, but none are directly relevant (you can see for yourself).
So, no reference at all to "engineering hull", "secondary hull", etc.
Next, "crawl". 21 hits altogether.
Here is the dialog that introduces the service crawlway.
SPOCK: As I recall the pattern of our fuel flow, there is an access tube leading to the matter-antimatter reaction chamber.
SCOTT: There's a service crawlway, but it's not meant to be used while the integrator operates.
SPOCK: Still, it is there, and it might be possible to shut off the fuel at that point.
SCOTT: What with? Bare hands?
SPOCK: A magnetic probe.
SCOTT: Any matter that comes in contact with antimatter triggers the explosion. And I'm not even sure a man can live in the crawlway in the energy stream of the magnetic field that bottles up the antimatter.
SPOCK: I shall try.
SCOTT: You'll be killed, man!
SPOCK: Unless a solution is found quickly, that fate awaits all of us.
SCOTT: Aye. You're right. What have we got to lose? But I'll do it, Mister Spock. I know every millimetre of that system. I'll do whatever has to be done.
SPOCK: Very well, Mister Scott. You spoke of the feel of the ship being wrong.
SCOTT: Aye. It was an emotional statement. I don't expect you to understand it.
SPOCK: I note it, Mister Scott, without necessarily understanding it. I propose to run an analysis through the ship's computers, comparing the present condition of the Enterprise with her ideal condition.
SCOTT: Mister Spock, we don't have time for that.
SPOCK: We have twelve minutes and twenty seven seconds. I suggest you do whatever you can in the service crawlway, while I make the computer study.
There's absolutely no reference at all to
where it is in the ship, except that it leads to the matter-antimatter reaction chamber that is a part of the fuel flow. The suggestion upthread by
@TIN_MAN that this is inside a nacelle is therefore reasonable.
https://www.trekbbs.com/threads/eng...rprise-revisited.297971/page-20#post-12853412
The remaining hits of "crawl" just mention the crawlway and are not helpful (you can see for yourself).
"nacelle" gets zero hits.
In any case, it's reasonable that wherever the crawlway is, it's where it can be jettisoned. Things that can be jettisoned canonically include, besides nacelles, the ion pod.