I can't answer your second question fully as I do not have much experience with JOGL or Java2D, but I don't see any reason for them to ever conflict or be cumbersome.
For your first question, I can definitely say that it depends. What's your target audience? Is your game memory intensive (Ever notice that many games have a high res/low res option)? Is this a game that will be available for vastly different screen sizes? If so you might want to provide 2-3 different "packages" of your assets, each scaled at a different size of the original (the largest one). The math to draw the images isn't as much as you think.
In addition:
If you build the game the right way, you wouldn't have to do much math at all. If you have some sort of Camera
class that takes care of the viewing of your GameWorld
then you simply have to scale the Camera's image instead of scaling each image independently.