I think it's mostly because, whilst they/them can be used to refer to singular individuals, it's much more common practice to use him/her. I'm pretty sure in school I was actively discouraged from using they/them when talking about individuals (even ones of unknown gender), actually. As for why people refer to Minako specifically as female by mistake, it's probably a mixture of it being PMMM (which has an almost entirely female cast), and Moid usually drawing them with a skirt (which is generally a feminine item of clothing, and thus tunes perception towards 'this person is female' regardless of whether it's true or not).
Though with all that said, by now it's been brought up and made clear enough times that people really shouldn't have to be reminded any more. I can certainly understand Moid getting annoyed at this point.