it seems like most of what antimatter produces is electromagnetic radiation and quarks of various kinds
Antimatter chiefly produces, upon annihilation, gamma rays. Said gamma rays have high enough energies to produce matter/antimatter pairs upon impact, though what kind of pairs are produced is largely contingent on the gamma ray's energy; most of the time it'll still just be electron-positron pairs. It
can produce baryon-antibaryon pairs but this is likely to be an extreme minority of events - which
specifically need to involve the uncontrolled release of antimatter as a weapon. Afaik, that's only a thing with one-two weapons in the game (the uh big red torpedo only uses antimatter as an initiation charge iirc) and also the Remnant pulse drive ship.
I don't actually know what free quarks would do to matter personally
Free quarks aren't really a thing. They can only exist for ridiculously minuscule amounts of time and IMMEDIATELY hadronize no matter what (it's called the strong nuclear force for a reason). The only quark that doesn't is the top quark, it's so ridiculously heavy its mass is the same as A WHOLE ATOM OF TUNGSTEN and the only reason it doesn't hadronize is that it decays
too quick for even the strong nuclear force to have time to act. Its sheer mass also prevents its easy synthesis in anything short of dedicated accelerator complexes and even then, it's not enough to have a macroscopic effect on materials' radioactivity by itself (or its decay products).