1) In trained hands, a standard microscopy could be better than a KOH smear. There are also other ways to ID an organism including PCR test, and the new nanopore machines.
2) Candida can embed itself beneath the surface in the submucosa. In those cases, it's extremely difficult to diagnose, and it may not show up in a scraping at all. Cedars Sinai only recently determined that this occurs in Ulcerative Colitis. In such cases, the body might make antibodies to it, or it might not. Nystatin in high doses is safe, but it may not help these cases as it only acts topically on the mucosal surface. Instead, prolonged systemic antifungals in high doses are needed (can be used in combo with nystatin)