Don't remember the exact volumes on top of my head, but the two more obvious are the "memory eater" story arc then the one with the mind reading creatures. Think those are past vol. 30, but not sure. Those two goes a bit beyond regular subtext and you can feel the authors went as far as they could get away considering the intented audience.
Though there's still ways to go, it's nice that western kid shows starts depicting relationships that goes beyond "here's a boy, here's a girl, both main characters, of course they'll end up together, that's how love work !" Of course I don't expect them to go too far with it, even with het relationship, those shows rarely goes beyond confessing, eventually a kiss and even those tend to be pretty rare, but gay characters being "open" with their relationship or love interest without going over the top are still kinda lacking.