It's common to hear comments about QA sites being "cluttered", "clogged", "spammed" etc.
Even disregarding advertising / off-topic astroturfing etc. (the sort of thing that the "It's spam" flag is intended for), I think that "spammed" has a subtly, but fundamentally different meaning from "cluttered"/"clogged" here.
In my mind, "spam" in this context means large amounts of self-similar content, in a context where that is unwanted or undesirable. There's a specific issue here that the axis of "similarity" might not be recognizable until after the content is already there. This seems to be the problem that r~~ is getting at.
On the other hand, "clutter" is anything that gets in the way when you're trying to find something else.
Spammed content (say, questions about a particular sub-topic) could potentially have that effect, in a limited way: if the front page of the hypothetical Pets community is constantly filled with questions about dogs, then owners of other sorts of pets might not only feel unwelcome, but experts on the care of those pets will find it that much harder to access questions where they can share knowledge. Of course the search is available to everyone, but only the dog experts will see dog questions immediately.
However, in my mind, there are two much greater categories of clutter: low-quality questions (the problem Olin Lathrop points out), and superficially similar, but actually unrelated questions. The latter can be hard to avoid for technical sites, for a variety of reasons (jargon might have heavily overloaded meanings; important keywords like
and could be common English words that search engines ignore or treat specially; a given error can have multiple unrelated causes in different contexts; etc.), but efforts should still be taken to ensure that "FAQs" can be easily found - both by users of external search, and by site curators.
When I have called Stack Overflow "cluttered" (or thought of it as being so), it's because I'm trying to close a duplicate question that I know is asked constantly, but I can't find a proper duplicate target - and my attempts turn up a large volume of totally unsuitable candidates.
There are a few tasks which I think are vital to avoiding such a mess (this list is what comes to mind immediately, but I'm sure there are more):
Experienced users should try to preempt bad beginner questions (based on the common gotchas that they know about from experience - I have written about this here before) by identifying the underlying source of confusion (etc.) and asking a good question about it instead.
Duplicates need to be closed swiftly and with fairly liberal interpretation of "duplicate". If a target is a near-exact match, consider whether the target's scope is inappropriately narrow, and if the question can be improved to avoid focusing on irrelevant details.
For computer-related sites, a question title should not be allowed to consist of only an error message. (There might be an analogous prescription for other sites, at least the relatively technical ones; but I don't know offhand what it is). It should at least either try to include a half-sentence summary of the context in which the error occurs, or indicate that the question is fundamentally about diagnosing the underlying problem, rather than fixing one specific such problem.
Ideally, every question would be approached from a mindset of "could this question, at least in theory, be used to close someone else's question as a duplicate some day?" If it's too specific to a single person's misunderstanding (or even just a simple oversight) then maybe it doesn't have value - at least in a main Q&A space; perhaps some Codidact communities will want a separate category for more personalized help.
If a question seems simply too low quality to use as a duplicate target, then improve the quality if at all possible. Hold high standards and keep on top of the quality issue from the get-go. We have seen how things play out on Stack Overflow for 15 years now; we have seen what they learned about question quality; we don't need to rediscover it.