the white chinooks have thrived since being transplanted from the harrison...they're an aggressive species that doesn't need to rely on the hatchery for survival... if not for fishermen targeting them, they would have decimated the indigenous populations (which now rely on the brood stock program for maintaining their numbers).
The red springs taken for brood stock are not indigenous as well (assuming you are talking about the July run). They are interior stock fish.
The actual indigenous population runs during steelhead season, which is why there are posters up everywhere showing the difference between steelhead and chinook. I have only ever seen 3 of these fish caught in the upper river. There was also a small run of the indigenous reds in the fall, I normally tag 1 or 2 every year that I fish the vedder. Seemed the last year before I left for college they were making a small comeback as I hit 5 that year that were reds, and were still chrome (some with sea lice) in late September.
O and clipped sockeye are solely to mark Cultus Lake hatchery enhanced sockeye. None are clipped for research that I know of, especially since the hatchery doesn't raise sockeye due to IHN outbreaks that they commonly have. They simply want to see if there is any actual wild representation left over.