I am using two types of things. Non gimbaled engines and extruded turrets. I would imagine the turrets would not leave holes but I am concerned about the engines.
I can't remember ever seeing holes from destroyed engines. They just lose some engine bell materials through damage that's it. For Turrets, they usually do. It depends.
If you've got vernier engines, they will poke a hole in the armor (obviously) it's strongly recommend to NOT have gimbals on vernier engines, as it makes the hole bigger. The same is true for turrets, assuming the turret gets destroyed, it will leave a big hole where the turret once was. Otherwise, an "alive" turret counts as armor (as poor as it may be, due to being a single piece, instead of a smorgasbord of material).