I had a 6990 running at 102 degrees 24/7 for about 3 months. It was fine.
If the fan stops, though - don't keep going despite the temperature looking fine. That's usually because the card throttles down to save itself. But with no fan, it will eventually hit "smoke poured out" state.
If the temperature worries you, you could manually up the fan speed of the card. They generally top out at around 48-50% of max speed under load. I had my 6990 set to flat 70% - It sounded like a jet engine, but at least I felt more safe keeping it on during nights!
If the temperature on your CPU reaches 99 degrees, I'd look into replacing the thermal paste between the heatsink and CPU. If that doesn't help, get a better CPU cooler.
In regards to watercooling, it does help keep the temperature (and noise) down. But it is an extra cost, and optimally, you should maintain a watercooling system by checking for leakage every now and then and refilling the water tank every few months.