User blog comment:Owlfeathers0117/Faction Defense Listings - PLEASE READ/@comment-27820070-20150609164345/@comment-27820070-20150609164918

Most super important installations are underground, with decoys (mostly just massive entrances just to get to the complex) to confuse most people. Decoys are made out of stone, coated with a titanium-looking paint.

R&D labs don't have decoys, but most of them are underground and have cloaked/camoflagued entrances.

Superfactories are buried even more deeply down (6-8km down) and reinforced with tungsten-titanium-vanadium-depleted uranium composite. They have stone mock-ups above ground, again, more decoys.

(There will also be defense turrets orbiting major colonies to defend them from attack...)