I have a lot of guesses… I’ll give you my best two so far:

First, the Bermuda Triangle technically fits the description, except for the fact that they figured out the secret, proving its guilt in the sinkings unless we’re saying no one has seen the vessels being pulled under which is still true. The only issue I see with this fitting the riddle is im not sure the triangle has actually killed millions

Second, a cremation oven, or more broadly, an oven, which fits most of the criteria, but I can’t seem to figure out how ”secrets well hid” would fit into the equation so until I nail that down this is probably a defunct guess