Any kind of missile or rocket that leaves smoke trails is chemically propelled, Ion engines don't leave that trail, neither are they capable of enough acceleration to cross a section of space in reasonable time (like, even slower than current missiles) Also, Ion engines don't work in an atmosphere, so you wouldn't be able to fire planet based missiles.
It's archaic technology compared to what other things are in Starmade, I'd much prefer is they just turned them into blobs of plasma being fired at the same speed as AMC's.