I think Patrick is spot on with his assessment that they weren't maintainable given the wind.
I'd also add that similar to Cypress Point, it must have become quite the pain in the behind to keep vegetation from encroaching.
If you think about the duneslike bunkers at places like Sand Hills and Pac Dunes, they at least have the fighting chance of being deep pits, generally shielded from the wind by being built/scarped/uncovered into upslopes.
The faux dunes at Pebble seem to have been built just below ground level, and I can't imagine they had much protection from the glazing effects of wind, rain, and human-wear.
The sand would have simply been blown everywhere, including all over those greens. At some point, someone likely decided that they weren't workable, and as cool as they look, that someone would have been correct.