The optimal brake temperature varies from car to car. The easiest way to check if the temperatures are alright is in the telemetry HUD. If the brake symbol is coloured in a really satisfied green, then they are quite right. If the symbol is blue, the brakes are too cold. On the other hand, red means too hot.
Just to be clear, are you talking about degree Celsius or Fahrenheit? 1000 °C is wayyyy too hot for GT3, but 1000 °F seems to be fine.
Interesting question. Personally, I am adjusting my brake ducts only to get my brakes in the optimal operating temperature window. Haven't noticed any effect on tyre temperatures but I haven't even paid attention to that so far. Would be cool to have a WMD member with a little bit more insight responding to this.