Gottago,
Sure, there are probably some unclipped hatchery coho. However, the Toutle River produces some wild coho in addition to those from the hatchery on the Green River. And there are increasing numbers of wild coho in the Cowlitz River.
The wild coho run from the upper Cowlitz was re-created by stocking hatchery coho fry in upper Cowlitz River tributaries. When those fry became smolts, they migrate downstream, and about half of them are intercepted at the Cowlitz Falls Dam fish collection facility. They are then trucked to the Cowlitz barrier dam for release.
Also, surplus hatchery coho from the Cowlitz salmon hatchery have been trucked to the upper Cowlitz River along with the returning "wild" coho that reared naturally in the river but started out as hatchery fry. Consequently, a lot of natural spawning by coho has been going on in the upper river basin the last few years, resulting in as many as 345,000 "wild" naturally produced coho smolts being collected at Cowlitz Falls for transport to the barrier dam for release.
If that isn't enough, some of the surplus hatchery coho have also been trucked to the Tilton River, above Mayfield Dam, producing even more (up to 76,000) wild coho smolts.
For the foreseeable future, the Cowlitz River is going to be a mixed stock fishery, with a lot of wild coho, and increasing numbers of wild steelhead and chinook in the mix. Although the number of hatchery coho smolts (4 million) greatly exceeds the number of wild smolts, the higher survival rate of the wild fish could result in wild coho being a much higher proportion of the adult run in many years.
You asked if there are any native fish in the Cowlitz. Yes, essentially. Although some fish were transfered in from other hatcheries on other rivers, most of the hatchery salmo broodstock used at the Cowlitz over the years were from native Cowlitz stock. Most of the hatchery steelhead were transferred in from Skamania and Chambers Creek, altho WDFW has kept a late winter steelhead stock from native Cowlitz steelhead.
Sincerely,
Salmo g.