Flatpak uses OSTree - a git-like system for storing and transferring binary data (commonly referred to as ‘blobs’), and that system works by addressing such blobs by hashes of their content, using Linux hardlinks (multiple inodes all referring to the same disk blocks) to refer to the same data everywhere it’s used.

So basically, whenever Flatpak tells OSTree to download something, it will only ever store only copy of that same object (.so-file, binary, font, etc), regardless of how many times it’s used by applications across the install.
Note that this only happens internally in the OSTree repo - i.e. /var/lib/flatpak or ~/.local/share/flatpak, so if you have multiple separate Flatpak installations on your system then they can’t automagically de-duplicate data between each other.