I've read that when a new Pope is elected, but before white smoke signaling the new papacy is sent up, the new Pope is lead to the Room of Tears to read a letter from the former Pope and he is ritualistically "crowd surfed" amongst the clergy to guarantee a man has been elected (I know the story behind that one lol). The Catholic Church has never denied that other secretive ceremonies also take place to signal the reign of a new Pope. Are any of these ceremonies known of outside of the Vatican? Are there any ceremonies the church won't comment on, yet we can be positive occur? If so, what is the most logical reason for keeping these ceremonies secret, and can we use what history has shown us about the election of a Pope to draw any hard conclusions?
I'm not sure where you heard of this. The Room of Tears is a small room off of the Sistine chapel where the newly elected Pope prays and dons his papal vestments prior to being introduced to the gathered crowds and after the white smoke has been used to signal. Named thusly because new popes would often cry at the responsibility now upon them.
There is no "crowd surfing" or gender checks. It's untrue and frankly more than a bit silly. The story you are referencing about "Pope Joan" is a wide spread but completely false story. Here is a prior link to a thread about this topic if you are interested with a great answer from u/domini_canes
https://www.reddit.com/r/AskHistorians/comments/2ramiw/how_much_is_true_about_the_female_pope_joan
The Catholic Church has never denied that other secretive ceremonies also take place to signal the reign of a new Pope.
One should be careful about drawing inferences from the unwillingness of any group, whether church, government, or private, to confirm or deny the presence of some internal activity. Oftentimes, the lack of denial is because the group has never heard of the claim, so to say that the Church has not denied something is not the same thing as an implicit confirmation. That's aside from the centuries of rumors, legends, and outright lies about the Catholic Church, such that the Vatican and its various representatives no longer address many claims the Church simply deems unworthy of comment.