They can do stool cultures, but that is mainly for when there is a specific pathogen they are looking for. Pouchitis is generally not an infection, but an inflammatory response to normal flora bacteria. Cultures would not show anything unusual.
Fecal calprotectin is a test that helps quantify intestinal inflammation. This might be what you are looking for.
Pouch endoscopy can show visible improvement.
We do not develop antibodies against antibiotics, since they work against bacteria, not our cells/tissues. They can become ineffective because the bacteria evolve to become resistant to the antibiotic. This is a major problem with antibiotics in general and why there is a big push to reduce their use as much as possible. Overuse of antibiotics are responsible for the development of "super bug" strains, especially in the hospital environment.