Maybe this is a bit subjective, but I think the superko rule is much simpler than the sort of ko rules needed for territory scoring. The only downside of superko is needing to compare against repeating any past board position, but in practice, the relevant history is often only 6 moves or less (i.e., it is exceedingly rare to encounter longer cycles than a triple ko) and it’s trivial for a Go server or program to help keep track. Regardless, I insist that superko is much simpler from a conceptual standpoint than the ko rules used for territory scoring.
For Japanese rules (I’ll address these specifically here, since there may be intricacies in how these differ from other territory rules), the simple ko rule is actually not that simple. First, long cycles can lead to a game ending with a “no result”, which is not the same as a tie or jigo, and requires the game to be replayed to get a result, or just abandoned, if replay is not convenient. Additionally, the possibility of no results from long cycles leads to some people getting confused about how exactly that works. For example, the sending two-returning one cycle (and similarly sending three-returning two cycle) is a case where a repetitive cycle emerges that should not end in no result, but I’ve seen cases where players misunderstanding the rules will believe that it should immediately cause a no result (before the player with the capturing advantage can eventually break the cycle after accumulating enough prisoners for it not to make a difference).
Second, many, many people wind up misunderstanding how the ko rule works differently when resolving life and death under Japanese rules. The weird thing is that a different ko rule is applied when evaluating life and death under hypothetical play (i.e., one that effectively nullifies the use of ko threats). Maybe the most common way this emerges is with understanding how to handle bent-four in the corner for Japanese rules. I’ve seen several cases of players getting confused about how to handle this, and misapplying the rules in various ways (e.g., insisting its a seki or requiring point-losing ko threats to be used in a game resumption). It gets even more confusing if something like moonshine life pops up, and I think you already know (based on other discussion in the forum), there are even subtle differences between how Japanese and Korean rules handle various forms of that.
So, in short, I would say that it is a big disadvantage of territory scoring that they avoid a superko rule, by instead using a combination of the simple ko rule plus loads of complicated special ko rules for handling longer ko cylces and ko in the life and death determination phase.
It’s also possible, and sometimes more convenient, to estimate the territory score, by counting the area. For example, on a small board, one might be able to draw a line cutting a board in half and count how many stones of each color line on or over that line.
AGA rules demonstrate how one can conveniently get the area score using territory counting methods with pass stones. Actually, on the matter of which is more convenient to practically count, I would say that area scoring has the advantage of flexibility, since one could use area counting methods, if one prefers, or one could equivalently use territory counting methods (with pass stones). Not needing to distinguish eyes in seki is another convenience common to various area scoring rules.
I think the scoring granularity issue is the only convincing argument illustrating a disadvantage of the common forms of area scoring rukes. However, if one wants to address that, one could use a simple variant of any of the common area scoring rules, by adding a button. This would yield scoring granularity of territory scoring, without all of the complex baggage that comes with territory scoring. Basically, something like New Zealand rules with a button would be much simpler than Japanese or Korean rules.
I think is just a coincidence, and the per capita popularity probably has more to do with population dynamics and overall size. One could also point out that Chinese rules are what the majority of Go players use.