Flatpak has runtimes, which is where most shared libraries are. There’s a common base one called Freedesktop, a GNOME runtime, a KDE runtime , an Elementary runtime, and more. (The GNOME and KDE ones are built on top and inherit from the Freedesktop base runtime.)
Additionally, at least for Flathub, they have shared modules for commonly used libraries that aren’t in runtimes. (Many are related to games or legacy support like GTK2.)
Lastly, some distributions are building their own runtimes and apps on top, so the packages they build are available as flatpaks as well. This is the case for Fedora, Elementary, Endless, and others.