Hi there,
My suggestion is to make the destroyer engine, active and special module hitpoint actually be influenced by the “Defence” lvl for PVE mission.
Loosing all module by any explosive / penetrating shoot on very high level is kinda annoying.
As far as I know it does scale with defense but I could be wrong.
Sadly nothing tell it clearly.
Apparently engine and special module inherit the resistance of the ship, but nothing more.(Special module - Star Conflict Wiki), but the wiki can be obsolete/wrong.