Generally, the hardware doesn't ignore those bits, so you'll need to mask em, and that costs some performance. All in all, it's probably a win, but it's not entirely free either. It really depends on what you're going to stick in those extra bits.
Java's assumption that you'll use those bits to address more memory is not a bad one; after all, for workloads between 4 and 32GB there's probably no optimization better than dramatically increasing memory density.
