”Ya no le quedan” Spanish has a funny way of the inanimate object being at fault.
It’s not the boy’s fault, in other words. Think of it more like, it’s a matter of fact statement. The boy is meant to grow, so he’s grown out of them, yes, but frankly it’s the shoes that simply just don’t fit anymore.
If you want more of a direct translation to include both sentences, it’d be “le quedan pequeños”.
“le han quedado” Implies they used to.
“Los zapatos ya no le quedan al niño. ¡Ha crecido!”
“¡Ha crecido el niño y ya no le quedan los zapatos!”