Pondering this issue, it occurred to me that given the relative ease of interstellar travel, and the superabundance of quirky individuals in the Imperium, it would be exceedingly rare to find a system anywhere near civilized space entirely uninhabited at any given moment. There would always be a background equilibrium population of transients occupying various bodies. These might be tourists on long-term holiday away from it all, or prospectors for minerals or Ancient artifacts, or religious zealots trying to found a new community far from the corrupting influence of sane people, or the Scouts doing a periodic re-survey sweep, or any of a number of other possibilities. I think this would be ubiquitous enough that passing ships seeing signs of small-scale activity on a "pop 0" planet wouldn't give it a second thought. This of course makes it much easier to hide more nefarious operations in "unpopulated" systems.