Loli is a Japanese slang term for “lolita”, which is a girl that has not reached the age of sexual consent. From the novel “Lolita”, by Vladimir Nabokov.
So yes, Nagatoro technically WOULD be a loli, but not when you’re talking about a boy only 1 year her senior. They’re practically the same age, so it’s not like he’s lusting after an immature child.