I think the main reason that the peeps earn more while the game is off is that the peeps are less likely to be distracted by random things like their kids switching lights on and off or rattling dishes, so they complete more work actions. At least, the AI calculates how many actions they would have completed, based on their experience and a few other factors, but not interference from the kids!

I agree about the illness - it's a nuisance; I'm also playing VV1 on my iPad at the moment. Every time I open VF2 someone is sick, often two more more. In VV1, with four or five times as many peeps, I only get the occasional sick villager, although admittedly they can heal each other provided a peep or peeps have enough medical skills.