RAW seems to indicate that they can, but I'm not clear on the exact definition of allied NPCs.
We have:
"Travelers: Travelers are all creatures who belong to the caravan with the exception of any draft animals used to pull the wagons. Player characters, NPCs, animal companions, mounts, and cohorts are all considered travelers for this purpose. Familiars are covered by their master as far as traveler count is concerned. Every traveler (save for passengers) provides a benefit to a caravan in some way."
So, at this point we know that they are considered travelers, but not much else.
Next:
"Travelers
Every person associated with a caravan who accompanies it on its journey is known as a traveler, and every traveler on a caravan fills a different job during the caravan’s journey—even if that job is simply being a passenger."
This is a little fuzzier, since it says "every person", but given the above, I think this has to count animal companions because at the very least they have to be passengers.
And finally:
"Jobs can be performed by PCs, allied NPCs, or NPCs hired for the position."
They're not PCs or hired NPCs - are they allied NPCs, or does this wording exclude them from holding jobs?