I can't recreate that issue but I'll look into it more.
For fine details:
Testing this in Sim.
Currently have four built-ins (via the Nadir's fixed mods): Surveying Equipment, HR Sensors, Integrated PD AI, and Integrated Targeting Unit.
Bug persists with or without additional modifications being added or not.
All large slots are filled with Tachyon Lances. All small energy slots are filled with tactical lasers. All the Medium Missiles have Pilums, and I've added a Locust Missile launcher for the large missile slot.
If PD drones are deployed, whether in 'standby' or 'free roam', the tachyon lances, when left on autofire, will track a target, but will not fire. I did not have this issue with High Intensity Lasers in the large slots. The drones have to be fully recalled into the ship for the lances to fire.