IIRC, TOS Shuttles:
1. Were FTL-capable ("The Menagerie")
2. Had "ion engine power" ("The Menagerie")
3. Under power they leave an antimatter residue ("Metamorphosis").
4. Their fuel requires a separate operation to ignite it ("Galileo 7") it would suggest that the fuel isn't antimatter to start with. This is reinforced when all the fuel is leaked out while they were on the surface and there was no antimatter explosion.
5. The reactor functioned with a substitute fuel supply could suggest that it converted their "safe" fuel into antimatter when running.
This could be applied to the Romulans. Their "power is simple impulse" can still be FTL and they could even have antimatter somewhere in the power generation chain.