The mechanical layout of the Uno and Due appear to be slightly different from what I can tell, the digital pins blocks on the Uno look like they are closer together than the same blocks on the Due.
Are there fit problems with a shield designed for Uno fitting on Due? It would look like the digital pins are going to have to bend a bit to fit.
I believe they are compatible mechanically.
The eagle files are all available, if you print them 1:1 and lay them on top of each other you can confirm yourself.