if you haven't added the flathub repository to your new debian kde desktop install, discover will only show you packages from debian's repositories that were automatically configured during installation.. even if you've added the flatpak 'backend' from inside discover--flathub still has to be added to your sources (see step 3 in link above).
once you have multiple sources of an application (for instance, 'vlc'), discover will add a 'sources' pulldown (top right, next to the 'install' button) where you can choose debian system package or flatpak (or snap, if configured).
which source you use is entirely up to you. on my own debian desktop, i usually stick with debs if it has what i'm looking for, as i've chosen debian and have accepted their pace at which new software is added. if i wanted 'bleeding edge' i would have installed something else entirely on it. but you can certainly go 'all flatpak' if you wanted to.