Question 1. I'm not sure I get your logic. Your house had windows, they got damaged, and now the money will replace them with new better windows? If you went from a vinyl window to an aluminum clad wood window, you'd probably increase the home value $200 per window, as compared to the cost difference of $200 for a vinyl window and $800 for a nice window. Your house value was X, then after the hail, X - $$$$, and now it could be X-$$$$ + $$$$, with the difference being probably 20% of the difference in value of the earlier windows and the new windows.
Question 2. If the roof is functional, just pocket the money, and replace the whole thing when it needs a reroof.