2 Euro cents. The single colour squares are easy on the eye to just scan down for the one that goes with your country/region category. I don’t look at them, just the category names since it’s been alphabetically ordered, so flags are nice dressing but would hardly look at them.
A few of the categories probably don’t have their own flags: LATAM, and Ireland (specified to refer to “island of Ireland”)
When I first saw the forum here, I was a little confused as to what was the significance of the current coloured squares, but got used to it pretty quickly, and I find the alphabetical listing now sufficient. Though I will add the disclaimer that if I’m looking through that list, it’s usually for Canada which is near the top!
As far as I know, only with custom CSS injected through a browser extension or similar. I’m not aware of a built-in Discourse setting which would allow users to disable them.
IMHO, since the current colored shapes are pretty much meaningless, using flag icons would be a strict improvement in the cases where that’s possible/uncontroversial (which I assume to be the large majority). For the remaining cases, the current shapes could remain, or the regional community could agree on a non-flag icon, e.g. some sort of symbol that could represent the region.
It depends whether people thing that having a “busier” user interface adds value - I would disagree with that (worse - a busier UI is harder to use), and remove anything like that that doesn’t add value. If the current coloured squares are meaningless, just remove them - don’t make the problem worse.
Similarly icons like the massive incandescent lightbulb next to “This Site Feedback” add no value. I presume that it’s supposed to indicate an “idea”, but that category is not used for that. Removing that massive icon would free up space for text that actually does convey meaning (like how “Foundation” above is shown).
Thankfully, the massive icons aren’t shown on mobile (apart from the misnamed “migration” category where it’s part of the actual name).