EDIT: IT WAS A CONFESSION?! I THOUGHT IT MIGHT HAVE BEEN...! But then why did she nod when he was like "the moon?"?!?! THAT IS CONFUSING MAN. CONFUSING! And I was like: Okay, it's just my fangirling heart moving ahead of itself. Because... I mean, Shouya is cute and a good guy (learning on becoming one, and that, in my book, makes him a good one) but I just... didn't know that Shouko would have a crush on him.
It was obviously a confession :)
She nodded because he mistook it as for "I love the moon" and it would be twice as embarrassing to say it again, and imagine it had to take a lot of courage to say it for the first time. About the crush on him, yah. I think that Shouko loved him since she first met him, i bet that she wouldn't do all those stuff if she didn't like him (and love him afterwards).
It's a confession 'cause in Japanese:
"suki" = I like you
"tsuki" = moon
They sound really similar, especially if you're having trouble pronouncing things correctly like Nishimiya. Also Ishida is thick anyway.