In the GitHub issue you mentioned "since people are confused [..]", but people are confused because your communication has quite frankly not been very good. Even today just looking at the Fathom README it's not at all clear that Fathom v2 (or "PRO") is an entirely different codebase/product which merely shares the name and branding, and not much else, and it's not clear that the "Lite" version is essentially unmaintained either.
Other places (eg Redash) do so, and are doing extremely well.
The change from FOSS to non-FOSS, especially throwing away the goodwill you'd started out with... makes no sense. :(
Popularity of DB Browser for SQLite wise, you might want to check our stats page:
https://sqlitebrowser.org/stats/
We're doing decently well, and our GitHub organisation has more active developers now than ever before. :)