I've been doing it for a while, with no problems (as far as I can tell). The folders are kept intact when exporting apps.

I have found when I have a lot of content in my data folder the application export has trouble migrating everything to the application folders. It seems like it puts all the data into memory before moving it, meaning if you have more content than memory the export will fail.

There was a topic that I had responded to recently, but I can't find it...

I may be wrong. I remember, around the first couple of times that I started exporting applications, that the application failed to start when using folders within the data folder, and that flattening the structure fixed the problem. Perhaps it was my error when trying to use relative paths, or perhaps a Processing bug that existed in 1.2.1 (or worse, 1.0.1!) that is fixed now.