I am fairly certain that whatever the number of changes as such - between your system and the most recent metadata has nothing to do with the freezes.
But as your observations are indicating some correlation - then there is so much more reason to disable pamac update check - to verify if this is indeed Pamac causing the system to hang.
It is fairly easy to create a systemd user service which runs checkupdates and display the number of lines
checkupdates | SYNC=$(wc -l) | if [[ -n "${SYNC}" ]]; then notify-send -u normal "${SYNC} package(s) to sync"; fi
You can create something similar to [root tip] [HowTo] Check if your AUR build scripts have been updated