Disclaimer
Flatpak uses OSTree, like Fedora Atomic Desktops (Silverblue, Kinoite etc) and similar to BTRFS snapshots.
So many files are deduplicated and linked, not actually there
https://gitlab.com/TheEvilSkeleton/flatpak-dedup-checker
50GB without
31GB with deduplication
21,4GB with BTRFS compression
I always use the app image if they are available. As for being slow I never noticed.
No app desktop entry is one on the reasons I like them. If its one I use a lot I make a hotkey to open it. But there are ways to add them. There is even a tool that makes its easy to do.
No updates. I’m not sure how exactly, but everyone I use auto updates when I open them. I originally had a issue of it breaking my hotkey cause the file name would change because of the version number going up. Which I fixed by using a *.