Especially with an Arch based distro like EnOS. It all depends on when your mirror that you are updating from has synced. In the past, I have run an update on my system and about an hour later, recieved a notification that there are updates an hour later. Why? because my mirror did a sync.
To safely check whether there are any updates use checkupdates script from the pacman-contrib package.
Do not check for updates using pacman or yay and just pressing n to decline updating. That has the same side-effect as running pacman -Sy, which is refreshing the local package database. That is not safe, and may lead to a partial update situation if you install any package afterwards. If you do that, update as soon as possible (with pacman -Syu), certainly before installing any new software.
To check whether there are updates to packages installed from the AUR using yay, it’s sufficient to run yay -Qua. That is perfectly safe.
Personally, I use a little script to check for updates when I’m impatiently awaiting for a package to be updated:
# Dependencies: pacman-contrib, yay
UPDATES=$(checkupdates; yay -Qua)
[[ "$UPDATES" == "" ]] && exit 2 || echo "$UPDATES"
# assume packages containing these strings in name need reboot after updating
if [[ $UPDATES =~ $REBOOT ]]; then
echo -ne "\nWarning: reboot after updating, just in case.\n"
Though, to be honest, on an Arch-based system, there is really no need to check for updates. There always are updates, unless you’ve just updated.