On the Enterprise, random numbering would be quite understandable: the numbers would be stenciled on the pods themselves, as no hatches would exist. The pods would probably be removed and reinserted every now and then; those of the Voyager were in fact launched and then recovered in at least one episode. It might even be that a given starship would mix and match her pods with a general Starfleet pool of pods of the same design.
However, on this particular ship type the explanation doesn't work, because the Voyager pods are indeed hidden behind hatches that don't leave the ship when a pod is launched or otherwise removed...
Perhaps we could argue that Starfleet stirred the pod pool before the ship embarked on her "Caretaker" mission, and stenciled corresponding new numbers onto the hatches so that the starbase crews would know which pod was inside at any given time. However, we get the impression that the Voyager sailed to DS9 and the Badlands more or less straight from her launching dock at Mars; why would there be a shuffle there already?
That is, one might assume Utopia Planitia would choose to install pods 1 through 72 in numerical order first, before mixing. But that may be a false assumption. Starfleet might just have picked the nearest 72 pods from the shelf and installed them onto NCC-74656, then checked which numbers those pods happened to hold, and then stenciled those onto the pod hatches.
OTOH, the multiple appearances of the same random number could be explained by saying that it's not a pod ID as such, it's a pod model ID. That is, the ship happens to have five pods from the 0047 series, sixteen from the 2703 series, and so forth. If so, there'd be no point in placing these models in numerical order, any more than there would be in parking the fighter jets of an airbase according to their designation, all the F-15s first and F-16s second...
Timo Saloniemi