Not sure on that. "engines" or "main engines" get said a lot, but I cannot think of any time they were directly referenced as being the same thing in dialogue. "power nacelles" or "pods" might refer to nacelles directly.
For easy reference, here is all the dialogue in question:
NACELLES:
The Doomsday Machine, SPOCK: The energy generated by our
power nacelles seems to attract {the DM}.
The Apple, KIRK: 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!
Bread And Circuses, SPOCK: {about the SS Beagle} Portions of the
antimatter nacelles, personal belongings. Captain, no signs of bodies whatsoever.
By Any Other Name, SCOTT: I have opened the control valves to the
matter-anti-matter nacelles.
The Savage Curtain, KIRK: Disengage
nacelles, Jettison if possible.
PODS:
Errand of Mercy, SPOCK: {on the Klingon attack} Blast damage in decks ten and eleven, minor buckling in the
antimatter pods, casualties very light.
Metamorphosis, SPOCK: {shuttle is caught by by the entity} Helm does not answer, Captain. / KIRK: Neither do the
pods.
The Doomsday Machine, SCOTT: We made a complete check on structural and control damage, sir. As far as we can tell, something crashed through the deflectors and knocked out the generators. Somehow the antimatter in the
warp drive pods has been deactivated.
The Apple, SCOTT: We're losing potency in our
antimatter pods. I don't think it's serious, but we're looking into it.
{and later} SCOTT: Scott, sir. Our
antimatter pods are completely inert.
I, Mudd NORMAN: I am in total control of your ship. I have connected the
matter-antimatter pods to the main navigational bank. A trigger relay is now in operation. Any attempts to alter course will result in immediate destruction of this vessel.
Elaan of Troyius, SCOTT: The
anti-matter pods are rigged to blow up the moment we go into warp drive.
MAIN / WARP ENGINES:
WNMHGB, SPOCK:
Main engines are out, sir. We're on emergency power cells
{and later} KIRK: Captain's log, Star date 1312.9. Ship's condition, heading back on impulse power only.
Main engines burned out. The ship's
space warp ability gone.
{and later} KIRK: Captain's Log, Star date 1313.1. Kelso's task, transport down with a repair party, try to
regenerate the main engines, save the ship.
Tomorrow is Yesterday, SPOCK: Engineering reports
warp engines non-operational.
{and later} KIRK: Captain's log, supplemental. Engineering Officer Scott informs
warp engines damaged, but can be made operational and
reenergised.
The Apple, KIRK: If you can't get those
warp engines working
Mirror, Mirror, SCOTT: I'll have to
tap the power we need from the
warp engines and balance it for the four of us.
Ultimate Computer, SPOCK: M-5 appears drawing power directly from the
warp engines, tapping the
matter-antimatter reserves.
Elaan of Troyius, SCOTT: Our shields will hold for a few passes, but without the
matter-antimatter reactor, we've no chance. Captain, can you not call Starfleet on this emergency? / KIRK: And let the Klingons know they succeeded in wiping out our
warp engines?
Tholian Web, SCOTT: Captain. We're losing power in the
warp engines.
That Which Survives, SPOCK: Can you give me warp eight? / SCOTT: I'll sit on the
warp engines myself and nurse them.
Lights Of Zetar, KIRK: Any damage to the
warp engines?
Savage Curtain, ENGINEER: Lost all power in the
warp engines.