there are only 2 windows which can not be prevented at 9to5mac:
1 Allow Notifications Y/N (this has always been the case and not new that this pops up)
2 Cookies Notification (this has been added within a few days ago; i presume in response to Europe's requirement)
on my machine/macOS i get no other pop ups on that site, and even these don't appear a 2nd time, except if you have cleared yr cookies/history in the interim.
you can control the pop up related info you allow in Safari/Settings for this website
and also check it via Safari/Preferences/Websites
at 9to5mac, i never get a window asking me to download flash or to update it.
and of course, i don't have flash installed on my machine.
I just loaded "9to5mac.com" and let it sit for a little while.
I received no "flash player update" message.
Do you actually have Flash installed? (I do)
If you have it installed, do this:
Open system preferences -- Flash Player
Go to the updates pane
Click "check now"
What result do you get?
Something else I would recommend (just something to try):
Download "Cookie" -- it's free to use for 15 days.
Install it and set it up
Set it up to delete ALL website data from your browser each time you quit
- tracking cookies
- webpage previews
- form values
- website preferences
See if this can get rid of the phony update message.