No, FB's graphics library does not support Wayland. I don't think wayland support is or should be very high priority for the folks working on FBC, since it's Linux only and no other Unix system implements it, including FreeBSD or macOS.
And it shouldn't matter either since Xwayland runs automatically on all major Linux desktop environments. Xwayland provides transparent support for X11 apps. I use KDE and X11-based programs run the same as they've always done. You can't even tell the difference between which apps are using native Wayland and which are X11 through Xwayland. Even ssh -X works transparently still.
Flathub's warning is needlessly alarmist. I think Flathub marks most flatpaks as potentially unsafe.