Simply, yes, reducing weight by, say, 1.5 lbs in the wheels will be more beneficial than from a non-rotating part. It's more than just the wheel weight though. Reducing hub weight carries almost no rotational intertia advantage. The rim makes a big difference. The tire and tube makes a big difference.
Still, at the rates we accelerate, even sprinting at 1500w, the rate of RPM change in the wheels is very gradual, so lowering the RI doesn't actually add much value. In seated acceleration, you'd never feel the difference between an average training wheelset and a lightweight carbon tubular. It could probably be measured though.