This only applies to the timestamp ("6 hours ago"), right? I think that's because the notification pop-up uses moment.js to render the timestamp, and moment doesn't know about $wgTranslateNumerals = false;

In T123845#1942978, @Catrope wrote:

This only applies to the timestamp ("6 hours ago"), right? I think that's because the notification pop-up uses moment.js to render the timestamp, and moment doesn't know about $wgTranslateNumerals = false;

Yes. The only problem I see is in the timestamps of the drop down menu. For example, mine now shows:
منذ ٣ أيام
(3 days ago)
منذ ٤ أيام
(4 days ago)
etc

Change 281187 had a related patch set uploaded (by Catrope):
Fix regression from 0fc63bde365: unbreak number formatting in short timestamps

https://gerrit.wikimedia.org/r/281187

Change 281187 merged by jenkins-bot:
Fix regression from 0fc63bde365: unbreak number formatting in short timestamps

https://gerrit.wikimedia.org/r/281187

Side-note: There's some details about this overall issue at https://www.mediawiki.org/wiki/Talk:Localisation#Languages_that_use_non-arabic_numerals_in_their_ToC - if any devs want to merge that to a better location, please do. (I put parts of it in https://www.mediawiki.org/wiki/Manual:$wgTranslateNumerals but I wasn't sure where else it belongs. Perhaps in https://www.mediawiki.org/wiki/Localisation#cite_note-6 ?)