If there was water ingress and it was powered up while that was in there, it's fairly likely there is damage to low-voltage parts (like MCU, gate drivers, etc).
If missing, that cap wouldn't stop it from operating, so if it is not working at all then it's not the cap causing that. Assuming it is a cap, and It's on the power bus it's just another filter for other frequencies than the big can style caps also on that bus.
If the part that's failed is not a cap across the power bus, but instead is a shunt resistor between the battery negative and the FET negative, then it may have exploded (vaporized) from overrcurrent due to shorted FETs (or FETs all being turned on at once) causing shoot-thru, connecting the main B+ to the main B- thru the FETs and the shunt.
I'd recommend tracing out the main power paths to see if that's the case, and then testing the FETs for resistance (there are various posts on that here, and also on the ebikes.ca site in the learn-troubleshooting section).