I had several boxes that cracked one year. I used plain old Wood Filler on the outside of the cracks. Some boxes had bees in it already. Then I just painted over with white paint. The bees glued up the cracks on the inside and had them filled up before I filled them with the wood putty. They were pretty quick on that. You might not worry about it. I took care of the cracks on the outside to keep water out and the wood from rotting faster. Once the wood putty dries, the bees should not get into it, and you can paint over on the inside if you want to cover it from the bees, but they will glue it up themselves. Something else to think of, even though it says non toxic, it was never tested on bees.
The only thing I can think of would bee beeswax or bee glue that would be totally natural for use in the hives. You could try that.