Good en masse, provided the ships you're shooting at don't have good shield efficiencies. Otherwise, they generally just tickle ships.
Perhaps repurpose this ion beam into something of a baby Tachyon Lance? I.E. Notable range, fair flux usage, low damage, no listed EMP damage, the trick being that it causes untold EMP arcs upon striking the hull? If you're using them on the shields, it's meh and borderline pathetic. BUT, use it on exposed hull?.. Well then I just don't know what went wrong. Everything went dead at the same time, boss.
That's assuming you know enough coding wizardry to repurpose the TachLance's special effect and give the ion beam a matching effect instead of purple and make it spawn numerous weaker arcs or maybe occasional destructive ones. Hell, even without the EMP effect, a weapon that becomes much more powerful if used properly sounds appealing. Oh, and burst, if that wasn't obvious by mentioning the TachLance. A continuous beam that arcs lightning sounds rather terrifying if grouped up like on larger Hiigaran ships.
Does the Rathan have twin light autopulsars or just a singular one? Autopulsars seems like a nice fit, looking at the orangey/yellow pylons that poke from it.
EDIT: Minor fiddles with post.
DOUBLE EDIT: More fiddling.