Yes you should.
Momentum sources are used to model fans, propellers or other fluid acceleration devices without having to model the exact geometry and motion of the device. When creating a geometry primitive, i.e. a cylinder, for the momentum source, you are defining which cells receive the specific source in the discretized transport equation.
Fan blades in combination with a momentum source constitute an obstruction in the flow path. The will divert the flow and induce swirl. Therefore, if you decide to use a momentum source, you should remove the fan blades.
For more information visit the documentation page on momentum sources: Momentum Sources Documentation
Here’s is also a helpful forum post on momentum sources in transport equations: How does Momentum Source work?