Why is she hiding his present?
Does she feel like it's inadequate compared to what he already has?

This seems to be a reference to something from The Melancholy of Haruhi Suzumiya-chan, but I've never read that series.

Yeah, she's essentially heartbroken because he's a popular guy and got a lot of chocolate, so she thinks her meagre gift wouldn't mean anything to him.

Considering that they're going out though, it's a bit odd of her to think that.

Considering she's Mikuru, it's not that odd at all, really.