It isn't only New York. Minnesota, Wisconsin, California, Arkansas and also private breeders charge royalties. The fees in NY go back into the breeding program, that is why there are two scales, one for residents and one for non-residents, all because there are some subsidies from NY and it is not fair to charge through your taxes and also in the royalties. Since you have already paid somewhat through your taxes, you get a discount.
For the most part, the grapes are intellectual material and copyrighted or patented. As for the non propagation agreement, it is sort of like having software like Autocad or whatever that you purchased but the creator retains the rights to it yet. NY has been cutting the subsidies like crazy in these economic times so I guess it is a small price to pay. They almost wiped out the IPM Program and we know how important that is to the fruit industry.
These take a lot of time to develop and test prior to release. When you see a numbered variety like 73.0136.17 (Noiret) or 70.0809.10 (Corot Noir) The first number is the year of the cross, so those would be in 1973 and 1970. Traminette was crossed in 65 and Chardonel in 53. Thankfully they are developing newer methods to develop them faster but it takes time and money. I know that literally 10s of thousands of seedlings have to be grown for each cross and grown to the point where resistance and quality can be evaluated before release.
Sorry for the long post but it always used to irk me to have to pay but now that I understand why, I am glad to chip in.