Been using yakima racks for about 20 years for carrying boats, bikes, skis, lumber, etc, etc.
The racks with the feet that sit right on your roof (like you will need) will eventually leave sort of dull outlines of themselves. You can minimize this by waxing the car -- no, it won't cause the rack to slip off if it's attached well. Besides that, they won't harm your car UNLESS you overload substantially AND hit bumps in the road while overloaded. Ask me how I know : )
I haven't had a rack that sits on the bare roof in about 7 years or so, so maybe the rubber feet are better now and don't leave a residue/mark over time.
The racks are worth the risk of damage. There is no better way to carry your stuff if you are a multi-sport kind of person. Oh...if you're going to carry kayaks, get the appropriate carriers (j-bars if you have short recreational or whitewater boats, cradles for longer boats)...and use straps. And if you're not sure of yourself, put bowline and sternline on.
The bike carriers with the jaws hat grip the downtube -- some of the models don't fit all the way around bikes with large tubing. My solution is to use a 2 foot cam strap to ensure it stays in place...and sometimes a bungee cord.