The real issue isn't Desktop vs. Web, it is "people don't want to run their own servers".
Take email: with Dovecot, Postfix and SpamAssasin anyone can build their own email server. Almost no one does.
With Syncthing or Owncloud anyone can build their own Google Drive, iCloud or OneDrive. Very few do.
There are alternatives to WhatsApp/Telegram where you'd create your own server (e.g. Matrix). Almost no one uses them.
Example: I prefer to run Google Earth desktop instead of Earth in a browser. It's faster, has more features and doesn't suck up as much memory.
I use Notepad++ instead of google docs for most note taking.
I use Kusto Explorer desktop instead of Azure Data Explorer.
Outlook desktop instead of OWA.
There are exceptions. The facebook messenger app I prefer in a browser, because, do I trust Facebook software to not scrape my screen and send it back to FB servers? I would much prefer it to live in my taskbar as a discrete app otherwise.
But a lot of things don't require internet connectivity at all, not inherently. They largely stay on one device and that's fine. If they're to be shared between people or devices, very often attaching them to an email is better than "share this link with your friends (all they'll have to do to see it is sign up for our service so Growth can report those sweet sweet activations)"
As with most nice things the bad actors (spam, phishing, etc.) in society will abuse things to the point that we can no longer have them.
I also don't have the requirement for anyone to be able to join a project-specific IRC channel I'm hosting. In fact, quite the opposite, I DON'T want just anyone to join it.
For secure communication, I still use S/MIME (I may be in one of the last clusters of people to do so.)
It's entirely possible this article was not intended for you. It sounds like you have different requirements than the OP.
Now, the cracks are showing in this approach, mostly because of the ones who do it poorly. Perhaps the ones to watch out for though, are the ones who do it well, e.g. Google Apps?
Eventually I gave up and moved to Fastmail. The few dollars per month are worth it.
Syncthing on the other hand I found pretty reasonable when I still had need for it, with my only gripe being that the only UI surfaced by several clients is a webpage which feels a bit janky.
Running your own email server is a pain, having a client that pulls down your emails and stores them on a NAS so that your email is only briefly stored in the cloud is not a pain.
Never used WhatsApp or Telegram so no idea what the alternative for those is.
And setting up your own email requires intricate knowledge of modern anti-spam protocols and reputation management.