Applications that are packaged using flatpak currently cannot use the smart card redirection in ThinLinc. Smart cards are yet to be properly supported by flatpak: https://github.com/flatpak/flatpak/issues/4723 There is some hacky support by exporting the host pcscd socket to the flatpak. But this is very fragile as that is an internal protocol that is not stable between distributions or versions of libpcsc-lite. The long-term plan seems to be to construct a bridge to p11-kit. I don't know if that will just work with ThinLinc, or if we need to intercept things.
RHEL 10 will package Firefox and Thunderbird as flatpaks, which makes this more relevant.