There is an abundance of scientific information that indicates hatchery reproduction genetically alters at least some salmonid species from there wild parents. This isn't even taking into account the loss of months or even years of in stream survival skills necessary for them to return as adults and spawn. Here are some links that support the hypothesis that hatchery reared fish have dramatically lower survival rates:
https://link.springer.com/article/10.1007/s10641-011-9783-5
Wild chinook salmon survive better than hatchery salmon in a period of poor production
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3352433/
Fitness of hatchery-reared salmonids in the wild
http://kintama.com/wp-content/uploa...rvival-difference-between-wild-and-hatche.pdf
Marine survival difference between wild and hatchery-reared steelhead trout determined during early down stream migration
I'd also note that this study found that hatchery steelhead smolts took
10 times longer to transit the river to the estuary than wild fish and had 3x the in river mortality.
In BC since the SEP hatcheries went on line anglers both in tidal and non-tidal water have reported perceived negative differences between hatchery salmon and the wild salmon they largely replaced; they were smaller, they migrated from the ocean to freshwater faster, they traveled deeper in the water column, they were less inclined to bite.
My own experience with cutthroat trout, coho and steelhead (hard to compare chinook since they are not marked) is that hatchery fish are usually significantly smaller, weaker (ie pull on the line) and visibly appeared less fit than wild fish . By less fit I mean thinner for their length, and more frequent damage to fins and skin.
Another concern is that hatchery fish by sheer weight of numbers may over compete for habitat, feed and spawning space, both in stream and in the ocean.