You need to take the boat back to the dealer. He should at least have a test tank or water test it for you.
When the engine is on the flushing devise the entire exhaust system is open to the atmosphere, just about any engine will start, there is no back pressure on the exhaust. When you put it in the water the water acts as a load one the engine. The engine has to work harder to push the exhaust through the water. It is designed this way. That's why just running on the hose after a repair like yours is not a good test at all. In addition the carbs must be syncronized and the linkage including the idle speed set in the water.
I would have a talk with the service manager or owner of the dealership. It specifies in the service manual to set these in the water.
As for your problem is is possible the carbs are just not right. Thermostats will not keep a motor from starting, they regulate the cooling water after the engine warms up.
When you start that motor you should be advancing the throttle. The engine has a primer system, when the fuel is under pressure, such as when the engine is turning over the primer opens a circuit and allows fuel to flow into the intake.
Advance the throttle or warm up lever about 1/2 way. Turn key to ON. Push key in, you should hear a slight click. While holding the key in turn to crank the engine. Engine should readily start. Once it starts you may have to push the key in briefly to keep the engine from stalling the first few seconds. Once the engine is running lower the throttle as low as possible without stalling the engine.
So in addition to talking to the service manager ask them did they do a compression test? Results?
Did they do a spark and timing test?
If the changed the thermostats, why if they didn't run the engine in the water? How could they tell they both were bad? Not likely. Why were the carb bowls changed, unlikely all 4 were bad. I would also contact Evinrude if you don't get good answers. Sounds like you were taken for a ride. Sorry.
Let me know how I can help further.