but what bugs me is that they calculated that the deepnet is way bigger than the surfacenet
The definition of the deepnet is all pages that are not indexed by a mainstream search engine like google, yahoo, bing, duckduckgo, etc.
A good 99% of webpages are not indexed by major search engines because no other websites link to them, and that's how crawlers work.
For example, my own website counts as part of the deepnet because it doesn't appear on a search engine. At least... I don't think it does.