How can I have blanks instead of 0 or NaN?
I don't think there is any other option. You can probably assign an empty scalar( [ ] ) but the size of D is going to change then.
And Is there a way to have the index D_{i}
I am not sure what you are trying to do there but why do you want to have seperate variables when instead of D_1 you can replace it with D{:,1}.
Hope this helps!