This sounds very odd. I recently upgraded to XWiki 13.9 and out of curiosity upgraded CKEditor to 1.56 just now, and I cannot reproduce the behavior (Debian 10/Tomcat9/MariaDB).
When you trigger the long query to the .../bin/get/CKEditor/MacroService do you see any high load on the server?
You should be able to force a thread dump to be written to catalina.out with a command like:
pkill -3 java
This might create lots of output, but the thread handling the request should have the URL of the request in the name (i.e. searching for MacroService should give you the stack trace for the thread busy collecting the macros).