A few months ago she declared "girls can't do physics". Where the hell did that come from?
Granted, I can't presume to speak for your niece, but I'm pretty sure if my parents had tried to pressure me at a young age in to something I wasn't interested in, such as nursing (to pick a similar parallel, as my mom was one, but it's definitely not my thing), I would have looked around at the abundance of women in the field, and the lack of men, and declared that men can't be nurses. Kids are very good at finding excuses.
So there could be social pressure for her to believe girls can't do physics. I won't claim there is or isn't. But just because she said that, especially because there's pressure for her to go in to physics, doesn't require that there be something holding her back other than her own interests/lack thereof, and or just pushing back. I've seen kids lose interest in things they should have been enjoying just because their parents wanted it more than the kids did, and put (to quote you) "inappropriate pressure" on them.
Now, if she's actually interested in physics (which I expect is hard to gauge at that age) and appreciates her dad's "encouragement", but honestly believes she can't do it because she's a girl, then yeah, there's a big problem there. But I'd be surprised if the pressure to go in to it isn't exactly the reason she said what she did. In fact, having written this, I have to wonder if too much pressure at an early age to go against the stereotypes might actually be doing as much harm as the stereotypes... Wonder if there are any studies on that...