Shoto is observant person. Even without trying, he notices the smallest details which he's using for his own benefit.
Being isolated his whole childhood made an impact on his character and made him a little awkward and too straightforward. That's why he's observing society around him to pick up some things, manners, and behaviours that might help him.
In school, pavement, park, shop - he's learning something everywhere. For example, do not point to other the mistakes of this one waiter in the cafe you both like to go to. Shoto hates this dead stare the waiter is always sending him...
But he notices one weird thing. When two people's lips are touching.
Every time, everywhere, there are at least a few people who are doing this. He also notices that this gesture is rather pleasant. These people always seem to be happier while receiving it. The ones they share this moment are the ones they feel comfortable with. Grins that are spreading on their faces, redness on cheeks that are sometimes caused by another kiss, additional hugs and soft touches make him wonder
Is it that really good? Will he also feel that giddy after receiving this like the guy he saw in the morning near lockers and was kissed on the cheek by another girl that made him literally squeak happily?
So, to find out, on a random day when you both are resting in your room, With a peaceful, yet still cute puppy-like face, he asks as if it were the most normal thing in the world.
"Can you kiss me?"
Shoto's not dumb. He understands what intimacy, touching is... but he doesn't seem to realise that that intimate kiss is reserved mostly for people you love...