If Big N implemented dual disc I think they intend it to be used it. It probably can't be helped how the drive reads the disc and makes noise. I mean if you ever reset the Wii you hear a little spin noise or something.
As for the dirty lenses, I think some are dirty, but that's not the main reason why Big N urge you to send your Wii to them, free of shipping charge, instead of sending out a cleaning kit or something. I read that some of the drive aren't calibrated to read dual layered disc right, so you need to send them in for Big N to fix that. Some might be dirty lenses, mind you, but like mentioned above it doesn't make sense Big N would go through all that just to 'clean lenses' that could get dirty again if the same condition is repeated.