I've no idea when or why Fender stopped putting them on their guitars, I would be interested to know, they don't get mentioned much on the website info.
They were probably removed by players because they tend to get in the way, & you cannot damp or mute any strings with your hand with the cover in place, a lot of it is down to choice & individual playing style. They also get knocked off & lost, which probably accounts for most missing from vintage guitars.
Two of mine have the original cover, but I remove them for playing, they just make the guitars look complete as thats what they came with.
