A sample of 1000 nonces might be too small though, it would be interesting to see the distribution along the whole LTC chain so far.
If you find any serious deviation from uniformity in SHA or scrypt, we all have some big problems. And I don't mean bitcoin, I mean the entire world. See here for a little bit on testing non-cryptographic hash functions. The crude tests described should be taken as "step 0" when looking at cryptographic hashes. Anything that performs poorly on them isn't worth the effort of explaining to the author why you aren't going to do a serious analysis of his pet function. Note that you've probably never heard of any of these algorithms, with the possible exception of spooky.
Also, this is the inverse of the idea in the original post. If there is an actual bias in the hashing function (and we hope there is not), then you can use that bias to make your mining more efficient. Of course, if everyone does it, then difficulty just ends up somewhat higher than it "should" be.
An analysis of the whole chain would probably require regularizing the data per difficulty since the range of nonces would shift as difficulty moves up an down - might be interesting unless it's very uniform....
The linked article is very interesting - maybe worthwhile to do a chi-squared test on scrypt - i don't think it's completely uniform since it uses HMAC SHA256 and SHA256 has been show to have collisions.
In any case probably time for me to dust of those stats books