One reason 2nd person novels are less common is that they can be a bit difficult to write well. It's challenging to maintain the 'you' perspective throughout without it feeling forced. Writers often find it easier to use first or third person.
The relative rarity of 2nd person novels can be attributed to the fact that it goes against the traditional forms of storytelling that readers are used to. First person allows for a more personal and subjective view, while third person gives a more objective and omniscient view. 2nd person is a bit of an oddball in this regard. It also requires a certain level of skill from the writer to keep the reader engaged without making them feel like they are being pushed into a role they don't want to be in. Moreover, publishers might be more hesitant to take on a 2nd person novel as they may think it won't have as wide an appeal as other forms.