I'm PRETTY SURE the safest place Botan could be in that town is beside Kurama, Yusuke, and maybe even Kuwabara. Yoko's name still carries some respect and fear among Spirit World residents and criminals. If anyone knew Botan was currently Yoko's girl, she'd have some serious perks--and haters-- for it. 

Well Kurama's hair is also pretty out there, so they're just Red and Blue together. I think the exotic hair also adds to Botan's natural charms, but I don't know how long she can endure her locker having a dozen confession letters each day. Maybe the attention is the catalyst that finally makes them come out and claim they're dating to ease some of the tension off of her? 

I think it'll get very popular once Kurama AND Botan are involved, but people give up within a week because it takes a degree of patience and tolerance that they weren't prepared for. It can be a serious subplot that helps Botan discover a love and affinity for flora, and helps bring them closer as people. And like you said, there will be some free time without the awkwardness of Shiori around (they love her, but it'll still be awkward if she walks in during an intense moment) to get more hands-on with this relationship of theirs. So we've got a lot of filler to work with until they finally close in on who is behind those suicides.