Dust in the finder is no big deal. You can get dust up there literally in a minute, or it might take weeks. I've gotten dust onto one of my cameras in a single lens change. Usually you can get it out trivially with a rocket blower, but even if it's on top of the focusing screen that's an easy fix too. (Or it might be trapped between the eyepiece and the prism, although that's not common.)
The worst case scenario, which you asked about, is that they are scratches or blemishes on the pentaprism. This would be difficult and very expensive to address. I've never seen that - even in F and F2 where the prisms are removable - but it could happen.
_____ Brian... a bicoastal Nikonian and Team Member
My gallery is online. Comments and critique welcomed any time!