If plug cables are healthy the engine will run as long as the airintake is above water.
The electronics behind the front cover seems to work fine, but the gen-light often starts to flicker when the alternator gets to wet (no worries).
I think the clutch is the worst problem, the clutch housing gets full of water and if you use the clutch (esp going uphill) it might start to slip.
It might be smart to find another way to vent the gearbox and final drive,
but itís not strictly necessary if you check/change the oil pretty soon.
When you drive in salt water you should clean your bike asap, corrosion starts fast (cables, bearings, leverage, electronics ++)