Dealer said it was my air intake
Sounds like another off-the-cuff, get rid of the PITA customer diagnosis from a "highly unqualified" H-D service department. Why would your particular air cleaner "whistle", when other's do not? And if you really do have an intake whistle, that would be a good indication of an air leak. Why didn't they check that out and fix it if that was the case?
To answer your original question, yes an exhaust leak could create what you are calling a whistle. So could a poor fit of the inner and outer fairing, or the windshield, or the lowers. There are many parts on the front end that could whistle if they don't fit exactly right. If you look everything over carefully and notice a gap that you think might make a noise, use some tape to cover the gap and go for another ride. If the noise is gone, you've found the cause.
When do you hear the whistle? All the time, highway speeds only, into a headwind, etc. The first thing to do to try to diagnose something like this is to make a list of the conditions under which you experience the problem, and what various inputs do to change the sound. For instance, does the noise stay the same with increased speeds or does it increase in volume or pitch? Does the noise only become audible above a certain speed, or can you hear it sitting at a stop? ETC.
Jerry