I think the main issue with the nvidia logo was that it was green, which goes with pretty much nothing. It's alright with my yellow mpower board, but green on blue or green on red is terrible. If the logo had been white nobody would've complained. But i don't think anyone would've complained if the logo wouldn't light up at all either.
The LEDs themselves aren't the problem if you can turn them off, it's the other design decisions which follow them. A hole in the backplate exposing an LED isn't nice to look at for example.