Tim,
Here is the deal. Air in your pond is good for a number of reasons. The one main reason is you need the D.O. to help sustain life in your pond. There are many others.
Fish will thrive and love you for it!
Air will help the already good bacteria in your pond do it's job better by slowly removing the muck you speak of. And if you add bacteria with air it will help it along even better.
The correct air system is a great tool and will help your ponds eco system and fish thrive. It will also allow you to have more fish than without air. And help you in those times when your pond gets a little low on water. Air is your friend!!

I have been running a system now for 4 years and others out here a lot longer than that and my fish look great are growing fast and are very active.
Here are a couple of fish I caught 2 weeks ago. Of course it's not just the air system that makes your fish look great and thrive but I believe it's a big part and a must for any serious pond owner.