It's the athmosphere that colours the explosion. Though I am no expert, but I dare to say reactor fuel has little or no effect on it. And even if it had, why would they use different kind of fuel (if fuel if even used)? Surely everyone would use the best one available. And before you bring up thruster colours, they can be explained by different engine design. Like the mechanics of producing the trust, temperature of the "flame" and such.
Multi coloured ship explosions look weird to me. Weapon effects are another matter alltogether, but for example a green ship explosion looks all weird to me, unnatural. Like in the B5 episode "A View from the Gallery" the alien ships make green explosions (explained by the athmosphere they breath). Sure it was colourful, but it didn't look right...
All that said. I agree that modder selectable explosion effect for ships would be useful.