Maybe but probably not. People that develop applications can save a major headache by choosing flatpaks so the ecosystem will gravitate towards it.
At some point new applications that didn’t launch a Linux version will do so but only on flatpak and older applications will start moving towards flatpaks since it’s less dev time.
It looks to me as inevitable that the best versions of an app will be a flatpak but if you’re on Ubuntu based system you can probably get by for very long without them.
Many of the problems with security and disk space are limited by flatpaks using same base layer for applications that is shared and easy to update.