just auto fire the weapons system and oxygen system (might need an auto-reloader and maxed weapons man)
even if the shields de-ion the Ion bursts will take it down b4 the weapons and oxygen de-ion
if the ships has a med-bay, just take it down with any weapon you have or risk using your Ion Burst on it.
i made tons of scrap from this tactic, i bought every possible ship upgrade (its a shame i didnt screenshot it

but then again getting even 1 Ion burst Mk2 is nearly impossible, i had to do this with the Torus ship cuz t starts with 2 of em,
hope this helps!