Is iPad Pro 12.9 compatible with 2nd gen Apple Pencil?

Yes. The 2020 and 2021 models of iPad Pro are compatible with the second generation Apple Pencil.

Here is the definitive compatibility list for Apple Pencil and iPad:

Apple Pencil compatibility - Apple Support

You should note the the first and second generation Pencils use a completely different pairing/charging interface - and can only be used with the specific models of iPad that respectively support them. The Apple Pencil models are not interchangeable.

See this compatibility list:--> Apple Pencil compatibility - Apple Support

To be sure that your iPad Pro 12.9" is a 3rd generation (or newer) model, identify it correctly, using these instructions:--> Identify your iPad model - Apple Support

Regards

Giulio