Because they break functions of commands.

If you replace one standard letter with a crazy character, and if that character passes in a command you use, it will cause the "unrecognized command" error.

For example; if I replace "s" with "š" with a quick text then I cannot use commands which have "s" in it like /assist.

Also because of this replacement, you can't send emotion sounds even through sound panel.

Shouldn't standard & script commands precede quick texts? Imho, it must be like this: If the entered text is not a standard command, then it will be checked for quick text operations.

well, many people use quicktexts to override commands on purpose so it will ahve to stay like this. You're right though that it creates the limitation you described. To bypass it, you could create another quick text as /aššišt that redirects to /assist .