I know the "you can never trust anyone who has affiliation links" argument, but if we follow that to its logical conclusion, Wirecutter should be strongly biased toward picks that give them the most money for referrals, and that's not really backed up by their choices. They pick cheaper choices pretty frequently, and it's possible to find picks where there's no apparent affiliate link at all, e.g., their pick for best "high-performance" subwoofer. One can posit, as was done in the thread you linked, that there might be deals directly with manufacturers that we don't know about, but "we can't be sure they're being underhanded without us knowing" doesn't actually get us anywhere useful -- the same could obviously be said about anyone, including CR.
In the review business it's better to be playing the long-term game if you're building a real audience. In Wirecutter's case their long term advantage is to make good reviews without regard to the affiliate payment.
There are already thousands of other websites that are just disguised ads. Wirecutter's differentiating features is that they don't do that.
They still have some reviews I think are pretty mediocre or products they chose that I think are bad, but generally I think they're worth looking at.
https://news.ycombinator.com/item?id=25993512
I like consumer reports. You pay money for subscription and they provide you a non biased review.