The term may have come from the fact that 'holystoning the deck' was originally done on one's knees, as in prayer. In realistic reference to their size, smaller holystones were called "prayer books" and larger ones "Bibles"; also, a widely quoted legend attributes the name "holystone" to the story that such pieces of stone were taken for use from St. Nicholas Church in Great Yarmouth.
According to one source holystoning was banned in the US Navy in 1931 as it wore down the decks (and with the demise of teak decked battleships became unnecessary). However, a photo on the US Navy's Navsource photo archive of the USS Missouri) purports to show Navy Midshipmen holystoning the deck of the USS Missouri in 1951 (albeit in a standing position) A Time Magazine article (June 8, 1931) discusses the end of holystoning (archive article (fee) ) in the US Navy.
John Huston's 1956 film Moby Dick, and most recently Peter Weir's 2003 film Master and Commander: The Far Side of the World, shows sailors scrubbing the deck with holystones. Holystoning is referenced in Richard Henry Dana's diary, the 1840 classic Two Years Before the Mast in what he calls the "Philadelphia Catechism":
The Baltimore class of heavy cruisers all had wooden decking in the area around and near the quarterdeck, and extending fore and aft along the sides of the ship. The USS Saint Paul (CA73) was the last of this class left in commission, serving in the Vietnam War as Seventh Fleet flagship. It was decommissioned in 1971. Her "cruise books" have many photographs of the deck divisions holystoning the wooden decks.
Holystoning in the modern navy was not generally done on the knees but with a stick resting in a depression in the flat side of the stone and held under the arm and in the hands and moved back and forth with grain on each plank while standing - or sort of leaning over to put pressure on the stick driven stone.