Or girl. Or neither. The gender of the child protagonist is undetermined, like in Undertale. My first instinct was that they are female, though – the “voice” is high-pitched and the closest name my language has to “Niko”, as well as the word for “cat”, are feminine.
The italics meant to illustrate some sarcasm, its meant to play off Niko's protests that they are not a cat. Given it comes up multiple times in the game, it seems like an obvious joke to make.
Same. Like most depictions of cat people are Japanese cat girls. And because the name is obviously inspired by the Japanese word Neko that on occasion is mispronounced Niko. On top of that Niko has overly long sleeves which is considered feminine in Japan. I came to the conclusion that Niko is female because she's Japan inspired and feminine at that.