Got to admit to being a noob guitar player but not to music. I am just guessing but the fact that a great many songs call for both techniques it's not so much cheating as changing the delivery of the note for a desired result. I would venture to say that working on clear note picking is not going to hurt you but to entirely replace hammer ons and pull offs would limit your tonal possibilities. Balance the techniques and find the balance that feels right to you. Now if I could play as well as all that sounded.