There are a huge number of noisy comments, and they generate a huge number of flags. But, a large number of flags are raised on comments where they won't do very much good: if there's only a few comments on a post, removing one of them doesn't make an appreciable dent in the noise.
Here's a fun chart:
The x axis is the total number of comments on a post (deleted or visible). The yellow line is the fraction of moderator-actioned obsolete and too chatty flags raised on posts with this number of comments. The blue line is the same, but cumulative, i.e., the fraction of such flags raised on posts with this number of comments or less. Data is for Stack Overflow during the past 356 days.
As you can see, over 50% of "noisy" comment flags are raised on posts with 5 comments or less. On average, that's well over 100 flags every day. The raw numbers are smaller on most other sites, but the percentages are pretty much the same (with the exception of a handful of sites where pretty much any comment turns into a long discussion/argument - you know who you are).
Now, don't get too fixated on the numbers here; the real cost is probably a lot higher, since some folks use "not constructive" for literally everything and I'm not counting those. My point is simply that a majority of these flags are chewing up moderator time in situations where they're not actually doing any good.
First, we need better data on this. Re-working the wording of comment flags (and dropping redundant options) should help there.
But then... I suspect we can easily get away with just ignoring "noisy" comment flags (those that don't indicate rudeness or some other serious problem) on posts that have fewer than 5 comments in total (deleted or visible).
To that end, we should hide these flags from the moderator flag queue when there are no "rude" or "other" flags on the same post, and when the post has never had more than 4 comments on it. Focus moderators' attention on getting rid of serious problems and removing noise when it actually obscures signal. The flags can hang around until more comments are posted or until other flags are raised... Or they can hang around forever, doing no more harm than the comments themselves.