Astro Galaxy - a realistic space exploration game

So iv noticed that when some has a ship in orbit and they attack you and fail you will attack there mines/weapons on the surface and go for capture/destroy instead of looting them.   

Well the defender always goes for capture / destroy in the attack, if there are attacker planetary / station forces involved. Only the attacker forces will go for looting, if he choose that option in the attack. Also, fortify bonuses apply correctly depending on what is happening, like if the defender goes for capture / destroy on the attacker planetary forces, the attacker forces will have capture / destroy fortify values, while defender will have the loot / plunder ones.