Here is something I would like to be able to do in Inkscape, which a colleague of mine is doing in Illustrator :
He produces multiple eps images and then load them into a single ai composition. The important point is that whenever any eps file is updated (overwritten with a new one), the ai composition is automatically updated.

In my specific case, I generate svg files from Matlab. Next I assemble them and 'beautify' them in Inkscape for publication purpose. However the images exported from Matlab will have to be regenerated every time the analysis is improved. And currently I am left with no other choice than redoing all the 'final figure' again in Inkscape.

So I suppose my question is as follow: is it possible to have objects in an svg file that points toward other svg files?

I thought svg_stack could be the solution to my problem, but changes in one element file don't seem to propagate to the main svg file.

This isn't currently possible. Scribus can do this by embedding the SVG, though it's not a perfect environment for working with SVGs. I have reported a bug that's related to your question here