Ships in the ME universe use ion engines (a real thing), antiproton reactions and plasma fusion torches, according to the codex.

It stands to reason that ions... wouldn't really be affected all that much by mass reduction? Ion engines don't really seem like they'd be affected much by mass reduction - they're simply charging particles via electricity, the mass of the equipment doing so shouldn't really factor in at all.

It's presumable the antiproton reactions and plasma fusion torches are also designed to not be affected by mass reduction if they work in similar ways. So long as the fuel being used contained the same latent energy regardless of mass, that energy could be siphoned off and . The plasma produced by the fusion torches presumably uses the energy stored in the plasma for propulsion rather than actually having a physical use for it. The antiproton reactions probably produce some large amounts of energy which can then be it isn't specified how this happens.

So pretty much, energy propulsion isn't affected by mass, so if you design the engines to not rely on any form of physical propulsion, it doesn't really matter.