Hello,
It will not depend on the encoder type, but on the coupling type.
If you have a cardanic coupling, the speed will vary along a complete turn, depending on the misalignment angle.
Obviously, the mean speed, integrated in a complete turn will be constant and equal to the motor speed.
If you use an elastic type of coupling, you can have torsional resonances, and the mean value of speed will be (again) equal to the motor speed. However, as the resonances are not ruled by geometric conditions (as in the former case) you can not warrant that integration on a complete turn will give you the exact motor speed.
With a bellows type of coupling, you can assume that the measured speed is the same that the motor speed.
Hope this helps and best regards!