If a program only wants to spend their time with their top few affiliates, they should simply become invite-only
If they are public, they should reply to all affiliate inquiries in a timely fashion.
It's true, the affiliates who bug reps the most generally are the ones making the least - but sometimes, the people ignored haven't even started their traffic or are "testing the waters" and that business is lost.
Another thing is, I believe reps should be split into two groups, to focus on what they do best. Most companies do not do this.
Group 1: Sales people. They go out and aggressively hunt down affiliates, do PR, board postings, shows...
Group 2: Affiliate Support. They manage your account, are generally more technical and can help you with your issues.
Very few are the ones who do an excellent job at both...so why force the rest to? Let them do what they do best.