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My project PCB has the bottom layer as a ground plane and the Pico sits on this PCB. Do you think is ok to connect all Pico GND pins to that ground plane ? And then, when a GPIO pin needs a GND reference, I take it from my ground plane, not the Pico GND pins ? For example, I have a GPIO pin that turns on/off a LED, or a pin with a PWM signal. Do I need to report those signals to Pico GND pins or can I report them to my ground plane ?

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It is unclear what dire consequence you expect ground loops would create.

You will find no practical difference if you connect the Pico ground plane to your ground plane - use 1 many or all Gnd pins (do NOT connect Analog Gnd).

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