Space Pirate Cargo Drone

From Metroid Prime 3: Corruption

Just a minor, non-aggressive labor drone in the Pirate Homeworld. Doesn't attack or anything, rather it spends all it's time lifting and moving some crates around. But it's also carrying something strange...

Hey, what's that above the eyes?

Oh dear, it appears to be someone's head!

This grisly secret is near impossible to see in regular play, as the tiny drones usually stay far from the player, but the game lets you 'scan' most objects to see the it's 3D model (as is being done here) as well as a bit of back story. Of course, the cargo drone's scan doesn't even acknowledge the existence of the strange little head, much less reveal any reason as to why its there. In fact it implies it's just a robot.
Things get even weirder when you look at the Space Pirate Militia model.

A perfect match, but doesn't explain why Pirate heads in the drone. Are they babies being transported? Is it a form of punishment?

Pirate Militia are slaves and criminals within the Space Pirate forces, and are notably thinner. Upon closer examination they look like an eel in a mechanical exoskeleton. Perhaps Pirates are naturally limbless 'eels' and have to rely on mechanical bodies, or perhaps the radioactive element Phazon the Pirates use in vast quantities atrophied their bodies and rebuilt them with machinery, or maybe the Militia Pirates had most of their body parts removed as punishment? Regardless, the Militia don't appear to be hampered in their movements.

Looking back at the cargo drone, the head doesn't appear to be severed (i.e. a beheaded criminal), rather it looks like a full 'eel.' Two prongs hold it in place, and may or may not connect into it's central nervous system allowing it to control the drone. It's still substantially smaller than the Pirate Militia.

Space Pirate tech as a whole is an unsettling mix of mechanical and organic that changes drastically from one game to the next, and the games themselves don't elaborate, so we may never know what's going on here. Perhaps that's intentional.