I'm not sure it's a great idea to have a water bowl in a beardie tank. Some people do it, but I'd worry it would make the atmosphere in there too damp, or that if he were very young he might drown in it.
As for putting his head under, is he moving his mouth while he does it? Sometimes they do drink like this, I've seen my bf's dragons do it in the
bath from time to time, his female did it on and off for a good couple of minutes just after she finishing laying her eggs, I imagine she was a bit dehydrated from the effort and the fact that she'd not really eaten much for a couple of days.
If he's not
drinking while he's in there, I have no idea, but my inclination would be to take the water bowl out and give him a
bath every couple of days if he enjoys it, rather than risk him drowning in it (if he's still a baby, if he's an adult and has always had water with him, then I guess he's probably fine, and maybe just enjoys it). I guess if he is shedding his neck he might be trying to soak it to make it shed more easily, but I've never seen them make the connection themselves that water helps with shedding, they always seem to prefer to rub the area on something.