So there was some code in kcmmisc which was inherited into keyboard daemon which sets the numlock state at KDE startup. Well the code had some ifdefs but it wasn't too bad and it was working (for me that is). Though users started reporting problems. As I could not find what's really wrong and latest numlockx (from which originally code was borrowed) was working I just reborrowed from the latest numlockx version. Seems to have helped... for a while...
New bug reports started to come in, with various degree of problems, including numlockx not working for everybody either (https://bugs.kde.org/show_bug.cgi?id=256255).
Some of those problems were caused by another programs reusing or controlling NumLock state/LED but some seems to be real with no obvious reason and thus no fix.
The summary? Well 300-lines program (numlockx) to simply set a flag for keyboard modifier and a LED might be one of those reasons why Wayland would eventually deprecate x.org
P.S. if anybody knows how to reliably set NumLock please speak up, 'cause I am giving up on this bug :)