I'm curious, what kind of problems? I see shops do it both ways in my area. In fact, one shop has a pretty elaborate setup where all tanks are submerged whereas another just has large plastic bins and another has nothing.
Let see, problems filling in a water bath.
After your first salty tank, your bath water is now slightly salty. After 100 tanks, it's brine. When do they change the water?
And getting water splashed on the valve, tank not purged, then connected. You've just introduced salt water into your tank.
And lets talk about water not compressing. Explosive failure, well water ain't going to protect you from the shrapnel. Though it will lubricate it for you so it hurts a bit less.
And cooling the tank? Yes you do cool the tank, but not the air. So your tank is cool, but it would still take 1hour, 30mins minimum for the air to cool. Hence your pressure will drop anyways after the air cools.
The only way to ever prevent a hot tank is to fill it 100psi/10 seconds at max. You should be filling 300-600psi/minute as the set safety standard.
So all these old thought benefits were actually disproved a long time ago. And Florida dive shops still allows their untrained customers to do cave fills. Never said the Dive Industry was perfect.
Those water tanks are actually a lot safer if they're empty when filling.
And also, ever have a tank fail on you when you're reaching over it to turn that fill knob?
There's a lot of bad setups of Fill stations.
Tank Fill safety is a relatively new thing in the history of scuba. Here in the US the only legitimate defense in court of law for HAZMAT (which scuba cylinders fall under as high pressure cylinders) is PSI training. And very few dive shops actually even read the material, let alone get the training for that. Let's not even talk about tank visuals.