and is there is an upper limit on how many files the unit Mk2a (12mb) will support?

I believe that the upper limit on files *per drive* is 131,072 based on this thread.

You can find out how many files (inodes) you have free by issuing a "df -i" command on your Empeg player. I can't imagine a situation under which 131,072 MP3's would fit on a single drive anyway. However if you had a LOT of small files on the music partition, this could become full.

It's not technically correct to say there's a 1:1 ratio of files to inodes, but it's close enough for these purposes.