There's a definite tension between the rule of not accusing other users of being shills and the reality that there are quite a few shills out there. I think it a still good rule, but not because it's never right. Rather, the rule is good because the false accusations do more harm than letting some shilling slip by.
Edit: actually not so silent - it's the latter part of this guideline from https://news.ycombinator.com/newsguidelines.html: "Please don't post insinuations about astroturfing, shilling, bots, brigading, foreign agents and the like. It degrades discussion and is usually mistaken. If you're worried about abuse, email hn@ycombinator.com and we'll look at the data."
It's part of the contract we have with HN users - we ask them not to post this stuff in the threads, but in return we always look into cases that they report to us directly.