[Fedora 39] Why does Discover say there's updates while dnf say there's none? Also, why does Discover need to reboot to install said updates?

Those updates in Discover are for flatpak, not dnf. You can verify that with flatpak update.

As for discover wanting to restart to do their update, that's a fedora thing for an extra level of safety while updating. You can read about it here.

Discover shows updates to both your flatpaks apps and dnf apps

Because those are Flatpak packages

Those are Flatpak updates. dnf can't see them I think.

happens to me in Arch with yay.

You can turn it off in the settings (may be system settings, think it's called offline updates).

It's a feature Gnome added and then KDE added too. Fedora isn't the only distro to implement it, but the most popular.

If the kernel, initramfs, or a driver is updated, you have to reboot the computer to apply them (you can't reload the kernel while it's running). A user might not know or notice this, so GUI installers (and some CLI tools like pacman on Endeavour) often warn the user or sometimes force a reboot.

Try this: "sudo dnf update ; sudo flatpak update"

Discover checks knewstuff (global themes, plasmoids, etc.), Flatpaks, firmware and snaps, (which all have a relevant backend package something like (discover-backend-packagekit). Discover, well more like PackageKit, will let you know if a reboot is necessary if there's something like a kernel update.

I had reverse situation, discover said there's none of apps i need or/and updates, while dnf was working flawlessly

pkcon refresh

Looks like flatpaks updates