European governments agreed that airlines would not be penalized (with cancelled departure or arrival slots) if they cancelled empty or nearly-empty flights. But airlines flew empty flights anyway.

From personal experience I know that many fewer flights were scheduled from the US to Italy flew in April and May, 2020. And many of those scheduled were cancelled a few days in advance.

Is it possible that the "ghost flights" started after May?

In any case, it is clear that governments ought to demand statistics about number of paying passengers, and publish them. The simple wish of a business to keep something secret should carry very little weight in the decision about whether to allow it to do so. Any significant public interest should be enough to override that wish.