None of what you just said would justify a hacking resistance. Him being "complex" isn't actually worth something. The way Cyn takes control of robots is just by waving her hand around, it's not some overly complex process where she has to manually go through and analyze his code.
I don't see Metal Sonic going around casually turning his hands into virtually anything or grow and shrink a pair of wings like a Murder Drone can.
Metal Sonic (in this key) doesn't have have High-Mid regen like a Murder Drone.
Even a regular Worker Drone has the chance to just casually revive itself, which is something
Metal needed outside help for.
Just look at the
Drone Physiology page and it's pretty clear that (Base) Metal can't even do like half of this stuff on his own.
Besides his resistances (which outside of resisting time manipulation, aren't very useful in this fight), Toon force, Spaceflight, and Power Mimicry, most of Metal's abilities aren't gonna be anything that Cyn hasn't already seen/used/made in some shape or form.
Metal Sonic can't
casually shoot five bullseyes in a row without even trying,
Metal Sonic can't catch a bullet with just the tips of his claws without even looking directly at it, N without any of his memories at all,
can barely land a landing pod upright when it was crashing headfirst towards to ground.
Groups of regular Worker Drones
can rework old machinery on a destroyed planet to make children.
So no, I don't think Metal is too "complex" for Cyn (not that being complex on its own, unless shown or stated, would grant him immunity to any form of hax).