You're correct, these are cases where organisations have asked FlightRadar24 to not display any data about their aircraft. In some cases you can still see an aircraft on the site with all identifying details saying "BLOCKED", but as I understand it you can request for your aircraft to not display at all.
This doesn't prevent you from seeing those aircraft via your own ADS-B receivers like directly-connected SDR devices, nor does it apply to any of the other flight tracking applications or services like PlanePlotter, FlightAware or PlaneFinder to which an aircraft owner would need to apply separately.
I can't say I disagree with FR24's position on this, seeing as though if they didn't offer it there would be a lot more pressure on the FAA and others to introduce an encrypted form of the ADS-B standard and because when ADS-B was introduced nobody foresaw consolidated services like FR24 which could provide not only an extraordinary level of crowdsourced data but also historical data.
This is a problem for air forces, which are are required to use ADS-B in certain areas but for obvious reasons don't want other countries to be able to see exactly when, where and how their aircraft fly. It's also an issue for private companies, where the ability to track the movement of corporate jets might give competitors extremely good intel on what a company's plans are based on where its execs are flying to and when.
This has only been compounded by the introduction of multilateration[0] which allows for aircraft using only Mode-S and without ADS-B onboard or activated to be tracked with the same level of positional data.
[0]https://en.wikipedia.org/wiki/Multilateration