Mud0ra

Hi there and good evening. I am replaying this old gem and i never really understand if these bonuses are just like achievements or they really "upgrade" your character?. Do they stack?. I got like 2 stealth bonuses, 1 damage bonus in certain missions. I tried to google and the wiki, even checked the forum but i can't really find an answer. Can someone with more expertise clarify this?. Thank you very much!