It's 99% safe to assume that the 5V PWM circuit in the BOB is protected via a resistor against over current even against a full short.

In a really quality manual, they would specify the protection method (ie, pull-down or pull-up or other) including isolation etc. Same on the motor driver side.

EDIT: Assuming said current limiter is in place, the worst case is that the driver inputs are too low of resistance and they end up seeing less than 5v due to resistor divider effects, possibly resulting in a loss of signal to the drivers.