"The Da Vinci Code" has a lot to answer for
Waiting for Sherlock to come on, I've been watching various PBS shows, one of which was all about medieval cathedrals. It was actually quite interesting. The problem was that it kept talking, quite ominously, about the secret codes built into the very structure of the cathedrals.
What they were referring to was the fact that the architects found inspiration in the Bible and in descriptions of other famous places of worship. Making your cathedral have two levels, one at 30 feet and one at 60 feet, just like Solomon's Temple is supposed to have had, is not "encoding." And when the architect describes his reasonings in a fairly massive book, going into detail regarding certain verses, it's certainly not secret.
And, frankly, it's not any more ominous than any large-scale religious effort in the middle ages and heck of a lot more benign than many.