If you want a healthy tree and healthy fruit (my favorite variety of apple is the Honeycrisp), then you treat it immediately. Apple scab does not kill the tree itself but wounds it and leaves it open for other things to do so. Here is a link that explains how it harms the tree and how to treat it (scroll towards the bottom to "pests").
It is important to treat a new just budding honeycrisp tree because it needs to be healthy. Treating the tree prevents it from acquiring any undesirable traits or diseases. There are specific products to be used for the process that you should verify before used. Visit an agricultural extension officer for more details about the products.