I already described the problem in Discord, as far as I understand, many people are facing the problem, so I decided to describe it here too.
The server doesn't shut down via SendRconCommand("exit") if it was started via nohup or systemd. If started via screen, it shuts down correctly. The last thing in the logs is always mysql.
List of my legacy plugins:
"crashdetect.so",
"sscanf.so",
"streamer.so",
"mysql.so",
"mail.so",
"tgconnector.so",
"mapandreas.so"
and pawnraknet as a component.
The problem has been present since approximately the last public release and is preserved in the current nightly builds.