There are suggestions that http://en.wikipedia.org/wiki/Planck_distance is the smallest distance (or size) nature handles.
You could say nature has no concept of real numbers.
No, no, no, you are over interpreting. The fact that you cannot measure with infinite precision doesn't mean it doesn't even makes sense to talk infinitely precisely about positions. You can for instance make thoughts experiments, by imagining an initial state infinitely precisely, then conclude that subsequent measures will give such and such results, this time with finite precision.
According to current models, nature runs on infinitely precise mathematics. (And according to most sensible current models, that math is also deterministic.) The fact that your access to those maths lack infinite precision doesn't mean the math itself is imprecise.
The measurement interpretation of the Heisenberg uncertainty principle is both a useful way to understand it, and historically, a way to ease experimentalists into accepting and believing it.
I only meant that we could describe (in principle) a hypothetical wave function with infinite precision. Meaning, at each exact point in our hypothetical configuration space, we would specify an exact amplitude. (With the usual caveats due to the fact that we're talking about a distribution, not a function.) From then, we could predict the experimental results, which are bound to yield finite precision.
Now, current physics say we will never infinitely accurately measure our wave function. But it also says that this wave function behaves lawfully, with infinite precision, from some (I think?) unknown initial state. Is there a problem left ?
Edit: it just hit me that there is a problem if you don't believe in Many Worlds. Just know that I think the Copenhagen interpretation is crazy (I don't believe in the collapse of the wave function), and that currently, I find some form of Many World Interpretation most likely.