Using an old eBike battery to power an electric trolling motor
It may be possible, it depends on the current requirements of the motor (compared to the maximum output of the buck converter). The ebike battery pack would also need to provide a little more than 1/3 of the current required by the motor (multiplied by 3 minus power supply loss by the buck converter).
A better idea would be to rebuild the 36V ebike battery packs into 12.6V packs.  You would need to add a 3S (12.6V) BMS to prevent over-discharge.  This requires caution, you cannot just split the battery pack in three and connect the three parts in parallel (you have to at least use bleeder resistors between the packs to equalize the packs before directly connecting them together).