If there are ten million Joplin users then there are ten million opinions as to whether any given update is critical. The first thing I always do with any piece of new software is make sure auto-updates are turned off. I like Joplin notifying me of an update so I can look at the fixes and then decide if I want to update or if it's just not worth the bandwidth to get it. As Steph pointed out, eventually auto-updating is going to cause a problem. Just look at the worldwide outages some of the big players have had recently with auto-updating. Hello MS 
This was on by default, I don't use this Joplin instance, and it was automatic.
However the tickbox Steph shows above was unticked, and upon ticking it, I got this when attempting to check for updates:
IMO it seems most of this from a Windows POV is the first popup could just be a little irritating if it appears say three times in a week as it would have this week; but that's rare on the whole, we're talking maybe 3 weeks a year after a new minor stable release.
I'm assuming the tickbox in settings is to attempt to make the experience more seamless by automatically running the installer? Joplin would probably make a good appx package for distribution in the Windows Store unironically, which would handle updates at a package level closer to e.g., Snap where updates just happen underneath people without them realising in the ideal case without interaction at all. Even FireFox has it going on.
Ok I think I know why. What if you restart the app after ticking this box?
It might, but we'd probably have to hire someone for it or generally divert resources. It's already a massive pain to release to the Play Store and Apple Store (for example, now the iOS release is blocked because Apple doesn't like our screenshots), so having to deal with Microsoft too it's not something I'd look forward to.
They can decide, as Google and Apple often do, that we need to upgrade one package or change our configuration or we're blocked, and they don't care if it takes us two weeks to do it. Free work for the richest companies in the world.
By the way : I reinstall the 3.3.9 in order to have a message when searching for updates...
The box "Enable auto-updates" is ticked.
If I restart JOPLIN => same javascript message
If I restart the computer => no more message. BUT when checking for updates : no more message "An update is available..." too !!!
I restarted JOPLIN many times : no update seems running...
I restarted the computer : same "old" version (3.3.9). No automatic update.
Maybe it's because of a portable version...
Anyway : no more javascript message and no more opportunity to know that there is a new version...
I don't use beta releases. That's also a lot of assumptions about what I would do without knowing me...
I'm sorry about that because it wasn't my intention. When I say "you" many times ("For some reason"...) it's maybe a bad way to "translate" the way we often speak in French Language. This "you" is informal and not the real "you"... Put "someone" instead of "you". Same thing with the "we"...
I just made a supposition about beta releases and workflow...
I understand =)