Well you can't really play any D on the fretboard, you have to be more specific, because keep in mind octaves. The tone might be the same but the pitch isn't. The staff can extend beyond the five lines, right? You can get notes way up and down it, so you can have plenty of Ds in sheet music that are specific about where you play them. It might sound off if you are supposed to play a low D and you play a D three octaves above what your're supposed to. But if it is the exact same note, (ie, open fourth string D and fifth fret fifth string D) then it's up to you where to play it, depending typically on what is more comfortable and easy.

Hope I made some sense... I didn't get much sleep last night!