I'd love to hide even more little things in the backgrounds, honestly - it's one of my favorite things to do. But I also have to balance that with how much time it takes. As fun as those details are, they can be surprisingly work-intensive, which adds up and slows down update releases.
As for the girls - you're right. Characters like Airi and Runa are more or less one-off appearances, and there are no current plans for them to return in major ways.
That said, the reason they exist at all is simple: without them, the world would feel empty.
Take Runa, for example. I could have used a generic silhouette character for her, and I actually did for her dad at first. It would've technically worked — but the scene would've had less, well.. character.
In general, you can think of most of the side girls in Crimson High as extras. They help support the main cast and make the world feel alive, but they’re not all meant to have larger stories. In fact, most of them won't be getting any lewd content, either.
The number of girls that actually matter is a lot smaller than it may seem at first glance.
Important to note, though: The distinction of whether a girl matters or not is not at all set in stone. It can (and will/already has before) change over the course of the story. Sometimes a side character surprises even me :P
As for why they're listed in the phone's character sheet: it’s mainly to help players remember who’s who, especially if they’re referenced again later. With a cast this large - and many of them having Japanese names - it can be tough to keep track, especially over the course of several years. Even core characters like Miko and Suzu get mixed up sometimes, so I figured having a reference is better than leaving people wondering "Wait, who was that again?" :)
Edit: Typo