Does the transformer in this circuit cause a voltage drop to the DC motor?
That's a current transformer. You may not disconnect the load on a secondary side. The circuit is for measuring the motor current, it does affect the DC voltage of the motor, but this voltage drop is neglible. If you want to eliminate it you have to short circuit points 3 and 4. You may never disconnect the secondary 1,2 or eliminate the resistances R46 or R47.