Rolls.......

How could I play the rolls on C, C# and D when using whistles in the
key of D?

In Grey Larsen’s book, Irish Flute and Tin Whistle, he goes into lengthy explanations of all the rolls. He states flat out that you cannot roll on D. As for C and C#, the rolls, if you care to do them, can be simulated by alternative fingerings for the C, and certain strikes standing in for the cuts. It’s complicated and he points out that many pros don’t even bother with these methods..they’re rather optional. I would have to recommend the book to you rather than trying to describe it here, since it would require some careful scrutiny.
Someone else have other notions?

You can’t physically roll on a D as there is no note below it…
Crans (an ornament borrowed from piping) are used instead (they can also be used on E in place of a roll). There are many different ways to execute a cran…I don’t recommend trying to incorporate them into your playing if you are a newbie/relative newbie. But it’s nice to know that they exist.