For the amount we run our pumps any direction isn't going to hurt it. If it were in use daily for long periods I'd install it with the motor shaft horizontally unless the bearings and pump head was designed to be run vertically. Sometimes the bearings in the motor don't like end loading and may cause premature failure. Also if the pump intake was pointing down and you had a 90 right on the pump intake it could cause issues in larger pumps like cavitation, but again our little pumps most likely won't be affected if you did have this configuration.