This can be anything from a poor setup, to a preference thing from the previous owner. Both nuts and saddles are replaceable, so if it bothers you much, bring it into a luthier and have him cut new ones (preferably out of bone) more to your liking. It is somewhat common to have the high strings closer to the fretboard than the low strings, but personal preference and individual playing style are big influences. Warped necks or other neck problems can be addressed by sloping nuts and saddles, but if this were the reason, it would have to be a fairly minor problem in the first place.
There is no value impact, as it can all be addressed by a good setup.
Kostas