Pretty sure lots of people have the programmer mounted on handle bars.
Never heard of one going south due to water/weather.
If you're really concerned though, mount it under the seat on top of the airbox.
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2008 WR250X
Gearing: 13t - 48t
Power Commander 5 / PC-V
Airbox Door Removed - Flapper glued - AIS removed
FmF Q4
Bridgestone Battlax BT-003rs