Let's hope I'm not reading too much into this, as others have mentioned that saying or using the phrase, "The moon is beautiful, isn't it?(月が綺麗ですね, tsuki ga kirei desu ne)," is you to tell someone that you are interested in. Cause it sounds similar to "好きだ(Suki da)/ 好きです(Suki desu) : I like you," the words : 好き(suki, like) and 月(tsuki, moon), have similar pronunciation. So it metaphor for love, and also one of the most famous Japanese folktale, Princess Kaguya, is about love and moon.
Now coming back to the actual point, Shounen saying that he can't see the moon, metaphorically and literally, might mean that he doesn't see his love for Onee-chan being returned to him. For him, currently, he knows that the Onee-chan thinks him of as a lil bro, shouldn't have hung up, Onee-chan wanted to say how she felt about him now.
Well I personally I think Onee-chan has feelings for him but she is just gonna deny it because of the age gap, and not completely realize her feelings until something happens. Now all we gotta do is just wait and see
F