Is there a comma before "and why?" at the end of a question?

If so, would I also put commas if a question ended with "why or why not?"

Ex: Are you going to bake cookies, and why, or why not?

No. As the sentence is written, "why" and "why not" are independent clauses:

Are you going to bake cookies, and why?

Why not?

Normally, you would put a comma before or when it coordinates independent clauses.

However, this guideline from Grammarly takes precedence:

When just two short grammatical elements are coordinated with or, do not separate them with a comma.

Searching the Corpus bears out this usage:

Are you going to bake cookies? Why or why not?