That little bit of shaft that you see probably means that you are too low for the shocks to handle and you'll most likely hit the bump stops if you hit a hard bump in the road. You might want to look into Ground-Controls extended top hats. They move the mounting point in the top hat up nearly an Inch(24mm) so the shaft has more room to travel. This will usually mean better ride quality and longer life of the shocks. Most only need it for the front, does the rear look the same for you?

http://www.ground-control-store.com/...p/II=642/CA=71

As for the springs, you got Ground-Control coilovers right? What spring rates did you get? Yes, very stiff springs CAN increase the risk of prematurely blowing the shocks BUT that's if the shocks can't handle the rates. For example, Koni Sport shocks can handle spring rates up to 600in/lbs, so any spring under that rate, the shocks will be fine. If you use 600in/lb springs or higher on the Sport shocks, you'll likely blow them out in a short amount of time. That's why Koni makes the "Race" shocks to handle rates above 600in/lbs.

So, it depends on the spring rate and shock combo. Your springs may feel pretty damn stiff, but they might be fine with those shocks. Also, in connection with the issue you first mentioned, the stiffer the springs, the less travel in the shocks. So that means if you don't have all that much room between the bump stop and top hat, you MIGHT be fine.

Find out the spring rates on your springs.