Is it bad to run a 1000rpm rated 12V DC motor at lower rpm?
Running the motor slower is OK.  The main limitation of how a motor is run is due to the heat it produces.  This heat is from the DC resistance of the windings carrying current.

The heat is therefore proportional to the square of the current. Since the motor torque is proportional to the current, you must be running the motor at a lower current to get the slower speed.

The above assumes that the mechanical load on the motor is no greater at the lower speed than at full speed.  The motor must also be able to generate enough torque to get moving from a standstill.  If it isn't allowed to move, and full voltae is applied, it can get too hot.