Make it count as a regular ship, however turrets wouldn't regularly fire on it. You would need to select target it.
My Idea for this is to require dedicated anti boarding ships. Perhaps the "magnetic grapplers" would have signatures, like docking points, that a turret could be configured to target.Third: Counters. This parasite-ship must have a way of being detected by the ship it is attached to (scanners?). It must still appear on the targeting sensors of other ships and be a valid target, attract heat-seekers etc.