I think (I'm not sure) that you can get shop-vacs with a HEPA filter.
I have hardwood, and my father bought me a Hoover Floor-mate for it... which I loved at first, until I realized how much easier it is to just sweep hardwood. Vacuum cleaners mostly just shove things around on hardwood; they don't pick up very much. I also bought a dust mop - the kind with a removable, washable cloth cover - to use in between moppings. I would get whatever you need for the carpeted areas, and not worry about vacuuming the hardwood; it's not worth it. Although a shop vac works great on smooth surfaces - I used mine in the basement on the cement floor before I painted it, and it was great.