These are good points. Do you think that if the researchers did find the sort of discretization that they are hypothesizing, that this would represent at least some weak evidence in favor of the simulation hypothesis, or do you think it's completely uninformative with respect to the simulation hypothesis?
I think that the simulation hypothesis does not permit any evidence for or against that does not violate the laws of physics. There's no way to distinguish between being in a real universe, a discrete simulation of a continuous universe, a discrete simulation of a discrete universe, or a continuous simulation of either a discrete or continuous universe with limited measuring tools.
If the laws of physics starting changing in dramatically interesting ways, I might see that as evidence of simulation... and now I need to reevaluate the evidence about cold fusion in that light...
If it is... I hope they do not crash the system with the test.
http://www.huffingtonpost.co.uk/2012/12/12/physicists-universe-simulation-test-university-of-washington-matrix_n_2282745.html
Be sure to check out the actual reseach papers linked in the article! I would have linked to them directly, but the article is full of follow-on links of considerable interest.