The topic of hidden Catholics in English society pops up a lot in works about the period (e.g. was Shakespeare a secret Catholic?), how quickly did the population accept Anglicanism? or was Anglicanism's resemblance to Catholic practice enough to keep most of the uneducated population thinking that the difference between Rome and London was the difference between Coke and Pepsi? What I am most curious to know is what sources and methods Historians have used to calculate the presence of a belief and practice that was not only hidden during the period, but purposely forgotten and swept under the rug by most of later descents of these Catholics who embraced the Anglican Faith. Any articles or books that deal with this topic would be greatly appreciated.
This general question of "how England transitioned from Catholic to Protestant" has been a significant scholarly debate actually. There are several books that you can find in the book list that directly deal with this area. Id recommend starting by having a look at The English Reformation by A G Dickens and The Stripping of Altars: Traditional Religion in England c.1400-c.1580 by Eamon Duffy. They essentially present a point counterpoint. Dickens basically argues that Catholicism was decaying in late Medieval/ Early Tudor England and that Protestantism was embraced as a popular movement. Duffy's counter, polar opposite argument, was that the traditions of the Catholic faith were alive and well prior to Henry VIII and that the reformation was imposed from the top down. The arguments have spun out from there since these two books were published in the early 90's, but Id say that's likely the best place to start in investigation this question.