What exactly did the old glitchdex have that the new one didn't? The old one was available as "glitchdex" while the new one was "glitchdex2" for the longest time. You just happened to arrive after the switch was complete. But since you ask, version 3 will not replace version 2 until it is ready.
And no, nothing is saved in pure HTML. The entries are stored internally as Melchior Format, a human-readable data format similar to YAML (but not as featureful) and is a variation of the format used in the Melchior research documents. However, with v3 there will be tools to edit this data easily without editing even the Melchior text. Glitchdex data hasn't been stored directly as HTML since the first version (the second stores it directly in the database).
What 2.3+ does with the Melchior text is that it creates the HTML on the fly and caches it, so that it does not need to be generated with each page hit. The index is also cached, because reading all of the entries from MediaWiki's database is taxing using the built-in API (since it actually seems to parse the wikitext with each successive get)