Ok, thank you for your help. I will reply with as much useful information as I can.
It is the most recent release of Joplin for Mac Desktop running MacOS Sierra.
Regarding the instructions in the notification section it says:
On the desktop and mobile apps, an alarm can be associated with any to-do. It will be triggered at the given time by displaying a notification. How the notification will be displayed depends on the operating system since each has a different way to handle this. Please see below for the requirements for the desktop applications:
Those instructions are then to either use growl, or follow the instructions I linked to in my first post which said which say to go use the Notification Centre.
I don't know how to run "terminal-notifier" would you mind pointing me to resources that explain it or kindly explaining so you so yourself? (much appreciated). I cant find it from putting into spotlight or searching in finder, siri doesn't have a clue and I dont know how to use terminal. The stuff you said before about reactive-native and Electon is all new to me so I'll have to look that up. I am a keen learner but have a lot to learn.
As mentioned before, it works for me, so most likely it works also for other people, so your problem might have to do with your setup.
This is good news as it means it should be fixable! 
Cliking your debug link and having a go there, in the desktop application instructions.
Unfortunately there no file called "flags.txt" so that methed wont work (this is me entering it into spotlight). Putting in the other one (c:\Users\YOUR_NAME.config\joplin-desktop) (obv with my name instead) doesnt do anything, maybe its supposed to be put somewhere else rather than spotlight. So I'm having trouble creating a debug log.
I had a look through the system log as you have advised but dont really know what to look for. In a single minute of activity (when the alarm was set) there are hundreds of things going on and none of them give me a clue as to being to to with Joplin. Any ideas what to look for there?
Also it may be useful to know that in the system preferences for the notification centre I have multiple copies for (for unknown reasons) of the same apps. It might be to do with creating a guest user account that somehow ended up with all the same applications but nothing else creating a possible source for the double copies. I removed the guest user though but maybe that is relevant, possibly, if not let me know and I'll call apple about that for help. I wondered if this was 'clogging it up', but I may be completely on the wrong track here.
Many thanks for your help, it is much appreciated .
