Unfortunately the flooring will have to come up. No matter what anyone says the urine has gone thru the flooring and is in the subfloor. Without removing all the source of urine the smell will continue to be there.
No, carpet cleaning only cleans the top layer of carpet. Urine penetrates through multiple layers in the carpet down into the carpet pad and the subfloor. Therefore, additional treatment is need to full remove urine odor.