Are AppImages a generel security risk?

It’s best to avoid them so I’d recommend reporting any bugs you find with the Flatpak to Cryptomator. In the meantime it might be better to install it from one of the repositories they endorse (PPA, AUR, Nix) if any of those apply to you. If your distro isn’t supported and you really wanted to avoid AppImages you could mess with Distrobox, but it can take time to learn and has its own downsides.