It won't really affect the growth of the java fern, but sooner or later, the leaves will grow back straight up, because they want to reach the lightsource, aka your aquarium lights.
Yeh, but the leaves will still grow upwards, so over time you may lose the 'tilt', that if you can get it to 'tilt' much in the first place. So long as the roots are exosed it'll grow prety much however you place it!