I was thinking of it as forward thinking way of doing things (taking my queue from python for which multiple version do end up being installed on most peoples systems). I would make /usr/include/d1 for d version 1 files /usr/include/d2 for version 2 /usr/include/d3 for version 3 etc. /usr/include/d should be a symlink that points to what is concidered the current version of the language.
I am not saying that it is the best way to do things but that is my thinking.