The hard to swallow part is that the pets themselves with the proper doffs gives a defense bonus other than that the way they were nerfed their projectiles are the only damage that is worth using them since their energy damage was nerfed so much.
Their debuffs are still valuable, IMO. Aceton Beam is something I'd never load but coming from a Fer'Jai it's decent. Danube Tractor Beam, of course. And I think the orion interceptors are way more useful than they get credit for.
But yeah, pet DPS is negligible. Spike is nearly so as well outside of a properly herded BoP decloak alpha, maybe an odd fer'jai tric, or a scorp torp volley.
Am I completely misremembering or didn't captain skills boost pet damage at some point? Was that back in the day when you had to pick your energy weapon flavor?