Parasites can cause very smelly fecals. Also, I've noticed that feeding a lot of crickets or supers will do it to. You may want to get their fecals checked if you haven't already done so.
Now, about how to get rid of the smell ... I use a product called Nolvasan. It has a very pleasant smell and the fumes aren't harmful to beardies like bleach and ammonia. You can sometimes find it locally at farm/feed stores. Or you can find it several places online. A pint will last you a while since you have to dilute it. And a pint usually costs around $13 - $15. A lot of vets use Nolvasan to sterilize their exam rooms and equipment because it works so well. And I just found out that it will kill the horrible yellow fungus that has caused many bearded dragons to become ill.
What kind of substrate are you using? Substrates like sand and bran harbor bacteria and tend to get smelly rather quickly. They need to be changed out frequently - depending on how fast the cage gets messy. I use the indoor/outdoor carpeting from Home Depot or Lowes and I take out the old piece and throw in a new one at least once a week. And I cut several extras so my beardies aren't without substrate for any period of time. Also I remove fresh poo daily. That way my cages never smell.
To clean the carpeting I take the pieces outside, hose off any debris, and soak them with a bleach/water solution for 30 minutes. Then they get rinsed off really well until no bleach smell remains then hung out to dry.
Hope this helps.
Veronica
Beautiful Dragons