By the spring of 1888, however, things were beginning to move. Johann renewed his contacts with various occult and chivalric orders, and, most important of all, he reconnected with his cousin, the Crown Prince Rudolph of Austria-Hungary. Rudolph, six years younger than Johann and Sauniere, was an unhappy, frustrated and idealistic young liberal heir to a vast, conservative and above all Catholic Empire. In 1888 Rudolph turned 30, and his father -- Franz Joseph had been on the throne for forty years -- showed no inclination toward sharing authority or including his son in the workings of government. This, in many ways, was the crowning frustration of a tortured and disturbed life. As a young boy, Rudolph's tutor, the Count Gondrecourt, bullied and abused him in a misguided attempt to toughen his nerve.
By the time he turned thirty in 1888, Rudolph's brilliance had begun to turn wild. Rudolph and Johann would be in continual contact for the next eight months until Rudolph's death. While the great secret, or even Rennes-le-Chateau, is never mentioned, there is evidence that Johann and Rudolph were planning some sort of coup. In the fall of 1888, Rudolph almost shot his father, Franz Joseph, "accidentally" on the hunting field. Rudolph was asked to leave for the day and the matter was hushed up. It was also the last time Franz Joseph saw his son alive. On January 30th 1889, Rudolph and his current mistress, Maria Vetsera, were found dead in the Imperial hunting lodge at Mayerling. Rumors leaked out that it was a suicide pact between the lovers. This was scandalous enough to quell any further investigation, and might just have been a smoke-screen. It is possible that Rudolph posed such a threat to the Empire that he was killed by the Imperial secret service.
Rudolph lived at about the same time but was married to a woman who did not interest him much and had a "love" relationhip with a woman,with whom he later died in a murder/suicide arrangement at his hunting lodge. He too was thirty.
I think that there was probably some weakness in Rudolph,spoiled and energetic he may have been involved in some shenanigans but your case for the Hapsburg's involvement in these silly but dangerous cults is weak.