I have two SB-900s (and two SB-800s) and shoot weddings with them. Yes, in the beginning they would overheat and shutdown when used heavily with the old style rechargeable batteries. That was solved by doing the following. 1. Turn off the thermal protection, you still get the alarm for a warning. After adopting items 2 and 3 I very seldom get an alarm. 2. Use Eneloop batteries or other low discharge batteries in the flash. 3. Use a battery pack for power. This takes the heavy load out of the flash.
As a professional, I don't want the flash slowing down. That doesn't work at a wedding. I'd rather have it shutdown and go to a backup flash. However, after adopting the three items above, I don't have it shutdown either.
John Herrel Nikonian from South Carolina See the light, capture the essence!