PlanetLab and the clouds are great ways to do non-reproducible research, because the other users in the system (where sometimes "the system" is the public Internet) create interference. Reproducible networking research either has to be simulated or has to be run on an isolated testbed such as Emulab.
The results from PlanetLab et al. may not be deterministic, but you should be able to reach the same conclusions based on repeated experiments. Otherwise, your results may be a little too fragile to form the basis of sweeping conclusions.
This may not be ideal, but it is no worse than any branch of science which is not purely digital.
