The best bet is to use the stencil method and paint the on the numbers. The stencil set that you can purchase includes a paint that is flexible and won't crack or peel off when you inflate and deflate the dinghy.
I know that most states and the fed require the state registration adjacent to the numbers, and there are plastic plaques that you can purchase for this purpose, but you are right back to the glue issue. I have those and purchased some pvc glue in a tube from Lowe's for a couple of bucks. It has worked well for the last couple of seasons.
Most dinghy owners around here do, in fact, attach registration tags to the transoms. Law enforcement folks seem to be intelligent enough to realize that the tags won't stick to pvc and don't make a big deal out of it.