Ahhhh.......the ol' Deschutes. I grew up fishing this river and will give you my 2 cents worth. I don't think the issue of steelhead returning is a virus thing.......it's a "number of smolts planted" thing. In the 80's, this was a gem of a river high and low because 1) WDFW planted more steelhead smolts back then and 2) You ALSO had some Olympia area fishing organizations planting smolts.....lots of smolts! as enhancement projects. Those plants have since been discontinued except for a puny effort by WDFW.
Same goes for the silvers. They used to be planted in Johnson creek in the upper river for a period of years so a self-sustaining run could be estbalished. It worked for awhile but over time, the run faded. Maybe this is where the virus issue comes into play....I don't know. I do remember alot of years where there were just as many silvers as kings in the holding ponds at Tumwater Falls.
As to Capitol Lake influencing returns, it's possible but it can't kill fish if there are no fish planted. The lake's always been a cesspool but it's filled in bad over the years thus making smolts more vulnerable to predators and warm water temperatures. They used to dredge the lake but gave up on the effort. I know it was alot deeper 20 years ago and that it didn't have the gross weed problem it does now. Smolts migrate before temps. get dangerously high and they pass through the lake fairly fast. (according to old studies I recall) The worst culprit actually used to be the Olympia Brewery causing thermal pollution(hot water released from brewery tanks) but the brewery's not a factor anymore and I think they cleaned up there act years ago when they were in operation.
Whatever the case, it was a cool river to fish. If you have good fishing now, it will be due to local knowledge and good timing to catch the few that do return.