Hi @duc.chunguyen, @jorge_garcia ,
Thank you very much for reporting this issue and so sorry for any inconvenient.
I will log an improvement about this.
By the way, I tried on EAGLE 9.6.2, and noticed even if we choose the variant which has hidden the part, in the CAM processor, there is a tooltip to remind the CAM processor will output all objects to PnP, regardless of current variant setting.
So the easiest workaround currently looks like to remove the parts from the generated PnP files manually as @gtoner2506 suggested.

Hope it helps a little.
Regards,
Helen
Helen Chen
Principle QA for Fusion 360 Electronics