First, it's likely safest to pretend they're not stored in the file system anymore. This isn't true, but may be soon. So, I'm assuming you like to use a script or other method to directly manipulate or read from files in 1.9.x or earlier Moodle Files areas. It's probably best to just not do this.
Nonetheless, technically, they are in fact stored in 2.0.x (well, at least 2.0.2).
A disclaimer: I'm determining this by glancing at the code and by some simple spot-checking. Although I'm fairly certain, I can't guarantee I'm right. Plus, this requires at least a passing understanding of Moodle code, files hashes and Linux.
The files are stored in your $CFG->dataroot dir., under the filedir dir. (at least they are in 2.0.2). They are named according to an sha1 file hash. See file.php in $CFG->dirroot dir. They are, within filedir, stored in 2 levels of dirs., the 1st being the first 2 chars. of the hash, the 2nd being the 3rd and 4th chars (only based on empirical evidence, not by looking at the code ... this may be incorrect if there are more or less files than our install) e.g., a contrived but illustrative example using the Linux command line from in the filedir directory:
% sha1 5x/29/5x294b696bd26a371afl95e32e05625fdf7da6cq
So, this file when uploaded was named myFile.txt and appears to have this name in Moodle, and when you do an sha1 hash on it, you'd get back 5x294b696bd26a371afa95e32e05125fdf7da6cd. So, the contents of the file in filedir/5x/29/ named 5x294b696bd26a371afl95e32e05625fdf7da6cq will exactly match myFile.txt.
For reading or accessing these files, you're likely okay. No guarantees, and use at your discretion. I'd strongly recommend against trying to update the files, as these entries are likely stored in the database, and any external changes could cause serious problems.
So, likely not the answer you were looking for, but it's also likely correct.
Before doing anything, I'd strongly recommend confirming my assumptions for yourself. Look at the related code, experiment on a development server, and find all documentation you can at moodle.org (I could only find http://docs.moodle.org/en/Development:File_API).