Sardines, Herring and Anchovies all have up and down cycles.
A conference I attended a couple months ago - hosted by a PBS scientist (the name escapes me right now), suggested that the ocean ecosystem never really loses biomass - the biomass simply changes. He said on warm years, you'll notice an increase in anchovies and sardines, and on colder years, an increase in herring. The overall abundance of bait fish as a whole in the ecosystem will not change.
The same was said for salmon. Chinook do not fair very well in warming oceans, but pinks on the other hand seem to be flourishing. Again, warming ocean conditions are extremely bad for sockeye and chinook, but seem to favour pinks. Biomass overall is the same - but not the way "we like it" as far as commercially important species go.
Going back to that paper - most likely the population hasn't collapsed - it's simply moved. California to Alaska use to have a high abundance from ~1900 - 1940, and then the population disappeared in the North and was only found in the South. The 1990's (ocean warming - salmon/herring declines) once again started seeing sardines return to their northern ranges.