I think as much as we want the dogs to have the protection of the double coat, heath concerns are certainly a valid reason to reconsider. I usually cut Honey's stomach hair down every year because she's allergic to flea bites and will tear it out on her own. She ended up with a staph infection from that when she was about 3, although it was much more mild than what you're seeing. Our vet had Honey on steroids until it cleared up and we got a medicated shampoo to wash her stomach with every day, and a conditioning lotion. Honey has always regrown her stomach hair just fine, the texture hasn't ever changed, so if that's the main area you're seeing the issues in, I wouldn't worry to much about trimming that down.
