I would go for a single drive. I think it would be less noisy. But this depends much on application I think. Two poorly decoupled drives can cause a lot of noise, but you could also let one drive sleep.
For future upgrades I think you are better of with the bigger drive though. Also cost is a factor; I usually go with what gives most bytes for the buck.
Both drives are almost equal in $ per GB. Right now the 2TB is $110 (newegg/amazon) and the 4TB is $200 (NCIX/TigerDirect).
I'm not familiar with putting drives to sleep. I don't think these NAS drives are designed to sleep like the Green drives. I've read a little of the sleep thread on SPCR which involves doing it manually, but I'm not sure if that would be bad for them long term.
Personally, I notice the combi/destructive noises caused by two HDDs far more than I notice the noise of a single "loud" HDD. HDDs, even of an identical make, rarely spin at *exactly* the same rotational speed, so you can end up with some weird acoustics. More of a problem if you're hard mounting drives, as the case tends to amplify. Just my $0.02
What if you mount the drives suspended? Do you think two drives that are 1/2 as lound as one drive would be quieter then?
The Seagate NAS drives are a nice example because they're exactly 3-4 db apart. and 3.something more db = 2x the loudness.
I'm also thinking that if you have 2x 2-platter drives. And you're accessing data off of one at a time, the other will be at idle.
So you have 19db idle + 21db seek
vs 25db seek (22db + 22db equiv)
But then like you said, they'd be at different speeds. I don't know if that would make more or less noise.