Yes, some conspiracy theories have been proven true.
For example, long unsubstantiated claims of government surveillance of private citizen electronic communications were later confirmed with the release then-secret NSA information by the Edward Snowden in 2013.
Prior to this, the Wikileaks organization, reportedly headed by Julian Assange, publicized the then-secret reports of international espionage back in 2006.
I suppose one could go further back to the release of the “Pentagon Papers” by Daniel Ellsberg in the 1971 having to do with the US fighting in Vietnam.
Depending on how one defines a conspiracy theory or what it takes to turn that into fact, there are probably a large number of them, though not nearly as many as there are bogus theories.
In the end, it’s hard to know what is true and what is false just by reading about a controversy. Most of the time, it pays to reserve judgement for a while to allow “the noise” to subside and the facts to come to light.