The problem with looking at how well shutting off hatcheries work, is that many people point to the Nisqually and the Puyallup. First thing to note, is that the South sound seems to be a death trap for most smolt. Reducing numbers probably did not help this problem at all. Second is that on the Nisqually, while there are tons of habitat projects going on and the commercials have raped the salmon runs in river. Sure, we could have good hatchery runs of salmon, but unless they are put back in the river it does no good. This likely has reduced the productivity at the same time the habitat was trying to increase it. Lastly, there is the problem of water draw downs.
Talking to a water specialist a few years ago, well levels were dropping for years, indicating a lowering of the water table. This dewatered a lot of small streams and reduced summer flows. They were going up last I heard, but I am not sure that the damage done can easily be fixed, especially with the all the other issues still not solved.