The NPC would burn through the missiles when the hearts were active unless you shut off the hardpoints or tell them to stand down. And if you tried to go head to head with a Cyclops in a fighter and get aggro, then the new aiming ability of the Thargoid would rip your little ship to shreds in short order. If you want to test what would happen just send your current SLF against a Thargoid and sit back and watch how long it lasts.
No. The only way this little fighter will be useful with NPCs at the helm is if you are sharing aggro and it can subtarget. The latter will never happen though because scrub combat pilots would call foul if they ever encountered decent AI.
I've noticed the NPC Crew fires off chaff constantly until it runs out, even if you're not around any other ships with it deployed. While they aim well with fixed weapons with a velocity when ranked up, they still aren't the sharpest tools in the shed. Their AI logic seems to be pretty basic when it comes to consumables, and shooting at targets.
That said, my crew does remarkably well with the fixed MC Condor, so the AX Taipan might not be bad beyond slow and pitching (40) about the same as my Anaconda (38).
An SLF with flak cannons would be interesting, though I expect it'd rack up oodles of fines and whatnot in an RES or CZ.