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.
For my curiosity, by the way, my account was rate limited. Thanks Dang.