Moved your post in "what did you do to your Ninja today?" into this section. 
To touch on your questions, the front end is naturally going to shift downward when you brake... its physics... transfer of energy and the shocks are absorbing that energy. Sport bike brakes are much "grabbier" than some other bikes as they are meant to slow you down in a real hurry. So it sounds like you just need to get used to riding a sport-ish bike and modify your braking habits. Not every style of bike rides the same. That being said there could be an issue... but just going off what your saying it sounds like the bike itself is ok. If you're concerned take her in for a check up!
To touch on your questions, the front end is naturally going to shift downward when you brake... its physics... transfer of energy and the shocks are absorbing that energy. Sport bike brakes are much "grabbier" than some other bikes as they are meant to slow you down in a real hurry. So it sounds like you just need to get used to riding a sport-ish bike and modify your braking habits. Not every style of bike rides the same. That being said there could be an issue... but just going off what your saying it sounds like the bike itself is ok. If you're concerned take her in for a check up!