As far as I know, it only hides dead (-4 votes) or flagged comments. You can enable them with the "showdead" toggle in your profile, as the sister comment correctly pointed out (I'd recommend doing so, to see through biases a bit).
I have showdead enabled, there are no dead comments on this thread and the current comment count matches the number of visible comments. I suspect the GP comment's observation was due to a timing issue
Hmn I dunno what it was to be honest. I checked multiple times and refreshed, at least I thought I did. Shrug. My app that I'm using has no settings to showdead so I wouldn't be surprised if the refresh didn't work as it doesn't from time to time.
Mainly because I have and use 5 browsers and can never remember which one I logged into. There is not a chance that I'll remember my password. I wish. There's just way too many. Also don't use a pw manager on my phone due to security reasons.