I would say there very much is an equal degree of fetishism towards boy's uniforms in Japan, uniform shorts specially are the characteristically "boyish" wear and you see this in boy character designs in animanga culture very commonly - a good random example is Ken Amada's shorts which conspicuously stay on even during winter. Hanako-kun is another, very recent example. I would say that the Meiji-Taisho-early Showa era uniforms are all iconic pieces in the shotacon repertoire, indeed even some of these most fundamental ones. Shorts don't mean the same across the board, though most everywhere it is a boyish clothing - shorts on a girl in China, per example, is tied with imagery of gender equality because of what it meant for girls to wear them as opposed to traditional female attire. The Shorts of Gender Equality, if you will.

The actual answer is that males are not as sexualized as females sui generis and this is true for all age groups, including those in school. So the actual question that we must look into to find your answer is - Is that due to patriarchy? The form it takes for us certainly seems like it, but we live in a patriarchy, so that's hardly helpful - let's try and go to times before that development then.

I'm not so sure that the prehistorical, pre-patriarchal "documents", i.e. artworks of all sorts uncovered by archeology, allow us to make that call: the first depictions of male and female sexuality are similar to each other, i.e. exaggerated large breasts and hips for women and enormous erect phalluses for men, both of which suggest the subordination of sexuality to procreation and fertility already. Outside of this, sex is always connected to death, like the ithyphallic Dead Man in the Lascaux caves. "Venus figurines" are far more numerous than the ithyphallic idols, so I would say that as far as the natural tendencies (as natural as human sexuality can be, of course, which is to say, not that much... human sexuality is erotic as opposed to animal and has been since the earliest times we have access to) towards sexualization of one sex group over the other, the prioritization has always been for sexualizing women over men, even well before patriarchy established itself.

Of course, we are talking about pre-patriarchal times, and as such the meaning of the relative scarcity of male sexual depictions comes down to the Paleolithic and Neolithic belief in the ultimate supremacy of the female over the male in matters of procreation - again, the shape of the Venus figures and the ithyphallic statues makes it clear that they are about procreation, and the prevalence of the former makes it clear that it was deemed most important.

So there would seem to be a general trend of overprioritizing the female element in sexual matters in both pre-patriarchal and patriarchal society. In Japanese culture, I would say that the fetishization of school outfits is likewise related to the idealization of the "peak years" of someone's life, when they are regarded as most vital and brimming, which in Japan is not around the early 20s but in high school. Compare with ancient Egyptian statues, which invariably portray the person its meant to represent according to youthful ideals rather than how they look in the moment - the Pharaoh is always in his mid 20s, you'd think.

Potentially, as a specific Japanese development, it may be tied with notions of ritual purity and thus "maidenliness": a notion that comes from the isolation of miko in their shrines so they can avoid that which is kegare, ritually unclean, and please the kami. The high school uniform then, should be seen as semiotically similar to the pure white clothing of he miko. This is a specifically female prerogative, much like the fixation on school girls over school boys. But in this case, then, it is just a culture-specific form of a fetish or idealization of maiden status, which are found across the board in all sorts of forms: here in Europe we don't have uniforms for the most part, the maiden ideal I think remains that of the "Persephone-type", from my rural experiences lol. The association of maidenliness with flowers here is probably nothing short of as old as the first civilization here, the Minoans, le vegetation maiden has arrived etc.

In any case, these kinds of things need to be looked into more, for all my yapping I have barely covered it, but I hope I've made my point that these things are just more recent forms and types of certain human preoccupations which are very ancient, and under them lie even more fundamental, generic bases on which they lie - i.e. the answer to why schoolgirls over schoolboys has to be sought in the answer of a potentially "natural" predominance of female over male period as far as human sexuality goes. After that, it's a matter of getting increasingly specific and what elements go into "the schoolgirl uniform" that make it such a fetish object, which is something that has to be approached both semiotically (i.e. what does it "mean", what does it "communicate", etc) and comparatively (i.e. comparing with equivalents from other cultures) so that we have a better idea of both why it is and why it's different to roughly equivalent things in its specifics.