I don't think making chemdraw a babel language is the answer here. The way I know chemdraw is as a standalone binary executable that is all gui. there is no scripting. maybe you could build an xml file by hand, but i would never dream of that! maybe I am missing how you would use it.
[[chemdraw:file.cdxml][file:file.png]]
Is pretty close to what I had in mind. I would define the link click function to just strip off the png, and open the file.cdxml for example, then you do not need both of those pieces. I suppose this means you would have had to export the file as a new png after editing it to make a change though.
The real examples I had in mind were some clean way to integrate emacs with my tablet and drawing pictures that are inline in a buffer. Clicking on the link would open the image in my tablet drawing program, where I would draw on it with a pen, and then save the figure. this is not all images though, just some. Hence the differentiation by a different link. In my course notes, I often have hand-drawn pictures in them. Right now I go through a somewhat annoying process of drawing in powerpoint, selecting the drawing and right clicking to save as an image, which I then put in as a link. I havent had time to find a much better solution. A link could save me some of that hassle, except that the link doesn't show in the buffer as an inline image.
I also wanted a "figure" link that would export different ways. For example in html export it would export as html, for latex as eps, and for pdflatex as pdf, but it would show inline in some supported format. I know I can use filters to do that on export to replace or remove extensions, but I haven't had time to write one, and I thought a link would be a nice alternative. We typically make all three versions (png, eps, pdf) of figures, and put the png files in org so they show inline, but we often have to switch them out to one of the other formats at the end for manuscript submission. A link like figure:filename that would somehow show inline if a filename.png existed would solve this problem.
Those are what I was thinking about for using other links as images.