The most effect way to solve the gross urine problem is to cure the underlying problem that is causing it. This requires diagnosing the cause of the itching and odor, and treating it. A second option would be to treat the itch that causes her to scratch.
Dog warts caused by a papillomavirus are usually seen around the mouth of young dogs and self cure within a few months. Older dogs get skin growths that look warty, but are usually sebaceous gland tumors. They do not get genital warts from papillomavirus
or other viruses as occurs in humans.
Most vaginal tumors in dogs are fibroids, leiomyomas or transmissible veneral tumors (tend to regress spontaneously). The surfaces get eroded, they itch and the odor can be very foul. If accessible, surgical removal might solve the gross odor problem. Have the warty growths been biopsied to determine what they are? Can they be surgically removed? What do the vets say about the vaginal growths relative to the odor problem?
Itching usually responds to corticosteroid treatment most commonly prednisone.If this is the only option and it works, the problem is solved temporarily. Prednisone doesn't always solve itching. It also increases drinking and urination.
Even though you don't see her as incontinent, urine is getting on her fur in some manner. This assumes the odor is urine and not caused by a vaginal discharge secondary to the tumors. If there is a component of older spayed female incontinence, which is very common, would a trial treatment make sense to determine if treatment helps? The usual treatment is phenylpropanolamine.
Let me know if this helps and if you have follow up questions.