Aside from Nanoha and Madoka, isn't there yuri in Yuki Yuna? Also, does Flip Flappers count? They're magical (I think), they transform (sometimes), they fight an evil secret organization, and they have a mascot.
^ Tougo is canonically gay for Yuna, and the gacha game takes the anime's nascent gayness and turns it up to eleven (there was a mock polyamourous wedding involved at one point). Symphogear also very clearly counts, being descended from Nanoha, and since I've exclusively heard Flip Flappers being classified as yuri before anyone mentions the magical girl stuff, I'd definitely say it counts. MadoHomu is... complicated- in Urobuchi's words, "I don't think it is that special -- a really strong friendship turns into a lovelike-relationship without the sexual attraction, in their case." Whether this is Urobuchi trying to make a valiant effort to represent homoromantic women or just him being physically unable to utter the word 'love' without adding in fifteen caveats is upto readers to decide. The fans, in many cases, very sensibly enforce death of the author and build the subtext into something beautiful, which might even be the intention- many franchises specifically don't make any ships canon so that fans can see all pairings as equal and mix and match to their pleasure (the official term, I believe, is open-pairings vs. closed pairings).
There's a part of me that wants to hope that if same-sex marriage gets legalized in Japan, a ton of the tiptoeing and uncertainty around homosexuality might shift, giving us a flood of canon pairings (in most CGDCT or magical shows, the subtext is already there, so all you'd need is to pen in a confession scene). However, even straight romance in Japan, despite being idealized, normalized and endorsed, is still portrayed pretty conservatively in most het manga, so I'm not very optimistic. Still, even if there isn't an overnight change, we'll probably get a lot more gayness in the next decade, since yuri's profitability as an additive to every genre is becoming increasingly harder to dispute.
