M.D cannon :yaknow form enders game
Molecular Disruption Device. The "Little Doctor" Can destroy any planet or star. Size of a missile. Good luck balancing that.
Web:a mine that destroys the engines
Easy. Just change its weapon damage from "normal" to "Engines only"
Internal goo - Phased shilding.
How about making it like my BuckTube Gel Armor? Then it is actually internal, and works against every weapon in the game (excepting Psi-Subverters) In your case, you could make it protect against Engine Destroying attacks too, since the AI can design ships with more than the legal limit of engines
It would be described as a honeycomb filled with high-damage-resistance goo, critical components are placed in core cells.
Photsynthsis glands:generates supplys from stars
Glands? Wouldn't it make more sense to have it be a Photosynthesizing Skin? Could be armor, or described as fitting under armor. Would likely come in very small segments, since it is nearly impossible to destroy the entire skin at once.