Practically every “awaiting” system update causes the desktop freeze unexpectedly: only mouse pointer is movable, the sound/music (if any) keeps playing, but nothing is clickable and nothing is invocable through the keyboard.
What I mean with “awaiting” and how it emerges in a time span:
In some day the system notifier shows a popup at taskbar like “there are available 9 updates”. My natural reaction is to ignore it to let more packages accumulated for a substantial update.
A few days (or a week) later the notifier shows something like “there are available ~200 updates”, later it shows like “there are available ~400 updates”. Then, in next few days I encounter an unexpected desktop freezing, and it does not usually tied to a specific event like “right after reboot” or “on resume from suspend”, - it just happens in a meanwhile.
So I have to only reboot, which is pretty bad cause of unable to save edited docs, coding results, finish critical download/upload data or finish messaging (sending correspondence) with someone.
Why does that happen and can that be avoided?
You might benefit from adopting a habit of not ignoring updates because they happen to be inconvenient. Some updates may be critical; newer updates may even depend on having already installed updates you ignored.
Being proactive can also help avoid these annoyances. Use the command-line to regularly update at a time that suits you; preferably after closing any open applications, media files, or documents you may have open.
It may also best to perform a full system upgrade via a TTY shell while at the Login Screen; before logging in to the GUI.
This command will request/perform a full system upgrade:
Interestingly, I have experienced similar annoyances; which were likely only coincidental. I don’t see how it might be connected to the Pamac notification, though. My guess is the accumulated debt of not having updated in a timely fashion must surely have contributed, however.
After that, can you suggest an alternative notificators instead of manual check?
By the way, regarding the correlation between awaiting accumulated update packages and freezing: sometimes Firefox gets freezing unrecoverably when it’s in the update list of accumulated awaiting packages, thus, it signals about necessity of update and formally acts as “anticipation/prevention” factor/indicator of the potential whole system freeze.