I changed my truck's exhaust from the standard 2 1/4" to a 3" system from the manifold, including replacing the exhaust brake. I do not know if there was any power increase, but if there was it is pretty minimal and not something that is "seat of your pants" noticeable.
I was not really upset by this, as the main reason for me changing the exhaust was so I could route it better, not to get more power.
If you have the opportunity, chuck the truck on a dyno before and after updating the exhaust and report back any differences.
The only problem with doing this is if you have a minimal increase in power you might question why you spent your hard earned on a new exhaust.
I also have a full flow muffler, and to be honest, it's not what I would call loud. Actually, unlike petrol engines, diesel engines are not normally all that loud, even without an exhaust.
A simple test would be to disconnect the exhaust flanges and remove the muffler. After doing that, take the truck for a drive and see if you notice any power difference.
That should be pretty similar to putting a 3" pipe after the exhaust brake and will cost you nothing to find out. That's assuming your muffler is positioned similarly to mine, which is pretty close to the engine/exhaust brake.