They definitely will. This manga is freaking old, and thus same-sex relationships are often subtle or censored due to publication. But her recent manga, super lover, shows the couple getting together. It doesn’t shy away from same-sex relationships, and if Komatta Toki Ni Wa Hoshi Ni Kike was released during this time, it definitely wouldn’t either. So I’m pretty sure, sensei has the same mindset as her fans. She want the two boy together too.
I always assumed (headcannon at least) that they ended up together so I am super excited to hear there is a more recent manga! I'm gonna look into it now!
This story is by far one of the best old school ones around for BL but the fact of the matter is, this story will leave you blue-balled and in the end the MC's don't even show if they get together. Again, wonderful story but man...I just wanted my boys to get together *cries into pillow*