Here are some data points, none of which I can verify the veracity of.
- According to a user on chiebukuro, some class at his school ran a crossdressing cafe, and some of the boys who would look decent in a maid uniform were put in a maid uniform.
- In this chiebukuro question, one user reports that they will be running a maid cafe at their school festival, and another user reports that she and the rest of the girls in her class dressed as maids for her class' cosplay cafe.
- This thread (beware: Japanese blogcancer) contains posters reporting that they had run maid cafes at their school festivals; some of those posters report having attended boys' schools.
- In this Twitter conversation, the replying user reports having done a crossdressing cafe where all the boys dressed as maids.
- Over here, one writer indicates that they have never actually seen a maid cafe being run at a school festival, but would not be surprised to come across one.
My conclusion: school festival maid cafes exist, but they appear to be quite rare. School festival maid cafes clearly show up more often in anime than in real life. (Unsurprisingly - you can dress cute anime girls up in maid outfits and they can't complain; real life people not so much.)
I do not have enough information to address the question of chronology - that is, which came first? Anime school festival maid cafes, or real-life ones? While it is well-established that maid cafes were first observed in real-life Akihabara (c. 2001), I don't know whether they propagated from there to otaku media, and then from otaku media to real high schools, or whether high schoolers replicated Akihabara's maid cafes in real life, and otaku media then picked up on them. My gut-feel is that the former is more likely, but either explanation seems plausible.