Yes, The Disney Stores still sell Disney Dollars. They currently have 1's, 5's and 10's. You can apply them to your shipboard account at any time during the cruise.
Oddly enough - as my DD9 was spending her money - she wanted to "pay down her balance" with her Disney Dollars. Guest services would not let her pay off her purchases without an adult present. This did not make any sense to my daughter who really was trying to watch what she was spending and trying to do the responsible thing.