What could be wrong with the truck if the exhaust pipes were under water for a few hours

Shouldn't hurt anything. Are you having a problem? Why did you change the starter?

Rain doesn't hurt the exhaust system. There's normally water inside as a byproduct of the catalytic converter doing its thing. That's why there's often a small drain hole in the back of the muffler, and it's why you often see water dripping from tail pipes. Anything more than that will just blow out when the engine is started.

When it doesn't start, what happens to the brightness of the head lights or dome light? Do they go out, get dim, or stay bright? If you get a single click and the lights go out, suspect loose or dirty battery cable connections. If you get a rapid repeated clicking, a loud buzzing sound actually, suspect a run down or defective battery. The place to start is by measuring the battery voltage with a digital voltmeter. It should read 12.6 volts if it's fully charged. If it reads closer to 12.0 volts, it's okay but discharged. If it's less than 11 volts, suspect a shorted cell and it must be replaced.

The headlights are a valuable symptom or clue as are the voltage readings. The starter wouldn't cause the engine to stall. That would be due to an electrical problem, with a sensor typically, or the engine is hydro-locked. Check for water in the air filter housing. If it's wet, remove all of the spark plugs, then try to crank the engine. Any water will be pushed out. If that's what happened, have the oil changed as soon as the engine is running again.

Depending on how fast the engine was racing when you hit this water, you could have a much more severe problem than you think. Water cannot be compressed so if sufficient quantity is sucked into the cylinder and the piston has enough momentum, it will instantly bend or break the connecting rod. I have replaced many an engine due to driving through deep water.