I’m on Manjaro also, and can confirm this also happens on my system (I just tried it), but I don’t have time to troubleshoot just now. Will try to later.
I have tested this further and disabling a font in system-settings seems to rename the font file to have a preceding “.” so font.ttf becomes .font.ttf. Additionally a list of disabled fonts is kept in /etc/fonts/disabledfonts.xml.
Each font I have disabled still appears in both native and non-native applications as OP has mentioned. I suspect this is a bug, but I cannot find anything similar on bugs.kde.org
Can anyone NOT on Manjaro confirm this is also an issue?
It seems that generated file /etc/fonts/disabledfonts.xml holds the list of renamed fonts from "fontName.ext" to ".fontName.ext".
But fonconfig is loading them even if they start with a point.
fc-list
/usr/share/fonts/noto/.NotoSansNagMundari-Bold.ttf: Noto Sans Nag Mundari:style=Bold
/usr/share/fonts/noto/.NotoSansTamilUI-Regular.ttf: Noto Sans Tamil UI:style=Regular
Even clearing the following cache dirs then running fc-cache -fv has no effect:
~/.cache/fontconfig/
/var/cache/fontconfig/
So, the mechanism adopted by Plasma to disable fonts by adding a point at the beginning is no longer reliable.
But if I created a test file in /etc/fonts/conf.d/99-disabled-fonts.conf using rejectfont tag and then run fc-cache -fv, it seems to effectively disable the desired fonts: