Whew, I sure didn't want to offend you with the question but I had to ask
No, I don't know a way to check for bad teeth, I have always used the smell test just like you are doing. Maybe look and see if any of his gums are red but this is just a guess.
My guess would be the vet will have to pull it. I have had 2 year old dogs come into rescue and we have had to pull 8 teeth...so sad but the dogs do okay and are much happier without the pain.
Just remember infected teeth can infect a Yorkies heart and other organs so in the big picture a pulled tooth isn't the end of the world.
Okay one other dumb question...What is your little one eating? Could it be from the food?