Yes, absolutely. You can have multiple header, nav, and footer tags sans penalty.
As long as you’re making sure you are using tags semantically and you aren’t putting them in invalid places (they’re block-level elements, so you can’t put them inside an inline element, for example) then you shouldn’t worry too much about what the sticklers are saying. It’s all to easy to get caught up arguing about tiny details instead of moving forward on your project.