I'm pretty sure that the item drop rate from kills with built in weapons is lower than the drop rate for kills with normal weapons (non-surgical). I haven't tested this thoroughly, but from my observations as long time wingship fanboy, I have much higher chance of getting a drop when the damage that kills an ai is caused by an equipped weapon.

If I had to guess, I'd say that kills with the built-in don't benefit from the piracy skill (I'm at 10 atm). While this is in-line with the exemption of built-ins from normal bonuses (damage, range, etc...), it doesn't really make sense to nerf the drop for built-in kills. Personally, I've been playing wingships since I started playing SS, and I was unaware of the item drop thing until I started using a real gun.
For example: I leveled from 220 to 350 on Slumberchromes, and for all of those kills I picked up 1 Fist of Light. Piracy was at 8 for most of that.

If this is a design choice and not a bug, it would be nice to give players some warning that built-ins don't produce loot, as it is entirely possible to get to level 800 with nothing but wingships.