This seems to have been resolved in 2.4.6 by T7151 or T7160. I don't really remember the details, but at least I don't see anything blocking system shutdown now.

If it were the case, I think that graceful shutdown of the system would need to terminate the client of scdaemon at first.

I also experienced hang on shutdown with GPG 2.4.1 and bisecting reveals that the first bad commit is rG2ccbcfec121f.