The articles you are referring to doesn’t show the full picture. In all protests only a part of the crowd is visible on the streets, the majority of the day is spent trying to get up to the streets from the MTR.
HKU has 15 years of data points on HK protests. There is reliable pattern of protestor organizers significantly overestimating and police mildly underestimating. Overall HKU and Police estimates are much more aligned. These two parties are actual subject matter experts vs protest organizers, ergo based on historic data and expertise, organizer estimates should be presumed to be less reliable / credible. Doesn't mean 2019 protests weren't massive. They're just likely half as massive as what makes for good headlines.