epub files are not planned to be officially supported at short term but you can still manually add them (their file extension) in the advanced options from the software. If CDS cannot extract them, it will at lest index their filename and path.
I’ve forwarded the suggestion to our product management team as an enhancement request.
This feature would be highly welcome! In fact, when I bought Copernic Desktop Search a few weeks ago I thought it had the capability to search inside epub and mobi files.
I was wrong.
Please include this option in next releases. For me searching ebook files seems a basic feature for an indexer in 2014, a task many other similar products can cope with!