I would like to know the answer to this as well as I am having the same exact problem. I had my phone in my pocket for hours today at work and had a message just sitting there with no notifications so I didnt get it til hours later.
Having same issues as OP with same steps taken to eliminate what may/may not be. Issue is only with the messaging app and started with recent late December update.
Post update, I noticed a change in messages that I might have recently replied/viewed saying something along the lines of "bookmarked unread messages here". Even if exit that conversation and close the app (task close & even force close/clear cache) the problem with intermittent / lack of notifications persists. I've even wiped cache in the bootloader menu.
Model is Samsung SM-a102u
Can I have your full model code and IMEI number via private message?