So I managed to kill the biggest bug, the Shield/shulker issue killing the commands from the system. Please help me verify this by doing the following:
Take enchanted shields & shulker boxes into the inventory and relogin. Test if commands like /home are working. If yes, the issue is fixed. If not, let me know in the comments.
On top of that, in the process of killing this bug, I found out a way how to get rid of a dependency in the code of Websend (which is running all our commands) which will make our live much easier in terms of keeping the server up to date for future versions.
So please let me know if you still run into problems of the commands not working.