how to model RF via hole in hfss

Your model should resemble reality as close as possible for accurate results. model vias as cylinders. You can use substraction to make openings in planes or layers.

Is it recommended to model the via as a solid cylinder or subtracting the drill hole with AIR?

the metal via is a solid metal cylinder. enable the material override checkbox if you are getting errors. metal will override a dielectric if they are both in the same space.