My guess, and it is only that, is that bunkers are added or subtracted by Greens Committee chairs, often according to the needs or problems of their own games.
There is a story (which I believe to be true) about Byron Nelson selecting the 11th hole at Hope Valley CC in Durham, NC as one of his favorite 18 holes from his 11 tournament win streak (he won the Durham Open there). At the time, there was a creek running down the length of the right side of the hole, and very much in play.
A subsequent green committee had the creek piped, apparently for no reason other than that they didn't want it in play. A number of years later, Ben Hogan was playing a exhibition with Mike Souchak at HVCC, and when he got to the 11th tee, Hogan looked down the fairway and asked what had happened to the creek. When told, Hogan is reported to have referred to Nelson's list and said "Tell'em they ruined a great golf hole" in reference to the greens committee decision.
There were also several bunkers added to the course over the years that Brian Silva removed when he renovated it a couple of years ago, most notably a savior bunker on the left side of the 4th fairway that kept hooks out of the same creek mentioned above.