I think the problem is the lighting (or lack thereof); the high-grade reflective tape can only be seen when you come from the shore at night, where there is light, but not from any other angle, which causes daily collisions (at night of course).
Some of these pipes are bent over and now rest under an angle, with the end just on or under the water surface, and even though they are not filled with concrete, they will probably pierce a polyester boat hull, providing the boat comes from the right direction.
The 2 or 3 markers put at Buena Vista point were in the middle of the lane used by boat traffic. I think they're gone now, due to the many collisions, although I haven't looked under the water surface.
It's difficult to suggest an alternative, because as you already said, lights will be stolen in no time, as will the safer, but more expensive floating buoys. On the other hand there is no need for as much markers as were placed. It goes without saying that no buoys are better than some of the hazards, that are there now... ask any boat captain that uses that route at night.