I just got the D500, and I am used to having a pop-up flash. However, I think I used it many times when I shouldn't have. Too lazy to pull out the big flash, and usually regretting that decision.
So, yeah, at first I was a bit confused looking down at the camera that does not have a pop-up flash and wondered if I made a mistake. (Of course, my personality doesn't let a decision be.) However, I planned on getting a small flash like an SB-400 or similar that would function better than a pop-up. I don't think I am going to miss the pop-up now that I am getting used to the idea of not having it, and I am hoping that I have better results because I won't be relying on it.
I analyzed this purchase for several months. In the end, I liked the tilt screen, the back-lit buttons and the layout of the camera. It looks similar to my D300, but it has many more convenient buttons. I wanted the capability to shoot birds and other fast things now and then, and I wanted the quick focus. I was willing to give up the pop-up, and instead, purchase a small flash for fill so I could take advantage all of the features of the D500.
I have an SB-800 if I need to use flash until I get a small one to chuck into the bag.
Hope that helps. You can only decide if you will miss it, but there is so much more to the D500 than lack of a pop-up.