On my home computer, I have the same situation as you. There are the old dictionary folders, with the gzipped html files, and the new zip-files, containing encrypted html-files (I did not check all, but only the E-E dictionary, dicthtml.zip).
I did the last synchronization of my reader via my office computer, which I cannot access in the moment. On my Kobo, the dicthtml.zip contains gzipped html-files.
Interesting point is: The encrypted html-files in the dicthtml.zip of the desktop application (home computer) are dated 07.08.2012. The gzipped html-files of the dicthtml.zip of the KT are dated 13.10.2011 !!!!.
I just checked:
in 1.9.17 they are dated 16.03.2012
in 2.0.0 they are dated 09.07.2012