I usually shoot with a lens hood, except on my 10-22mm...because that lens hood is huge (wide) and doesn't block much light.
I like lens hoods because they protect the lens from light but also from bumps or drops etc. When indoors, you usually don't have to worry about stray light affecting your photos...but the protection aspect is still nice. Flash or no flash, it shouldn't matter...as long as your hood isn't too big and your flash isn't too close to the lens...in that case, the hood might block some of the light from the flash.