There are several places water gets in Airheads. the most famous is the speedo cable boot on the transmission. Water can also get in the carbs but I don't know how it gets in there. Running down the intake tubes maybe. I found water in my final drive last year, still don't know how it got in there. If there's water in the gas it separates during storage and rusts the bottom of the gas tanks. Rusts them right at the seem along the bottom.
The timing window is for looking at the edge of the flywheel for finding TDC and ignition timing. This area is open to the out side on the bottom. It's not sealed. Not very likely water would do much damage except rusting the clutch to the flywheel and the pressure plates. Have you worked the clutch to see that it works yet? I know you have started the engine. If the flywheel is rusted to the clutch you will think there is no clutch. If you can push start the bike in second gear and try revving the engine and trying to shock the parts apart. Try revving the engine with the lever pulled in. Sounds worse than it is. It is the standard way to unstick a clutch that's rusted to a flywheel for any machine, not just Airheads. And surprisingly they usually do survive if the clutch wasn't worn out to begin with.
Seat latches and seat locks are often in disrepair. Look at a parts fisch and you might get an idea of the complication. Mines been messed up for years. I need a complete usable latch to start with I think but I make do with what I got because it still works, sort of.