Should it be washed every time they empty the food bowl? Every few days? Does it depend on the species? Are there any dangers to not washing the food bowl at a more regular time than the recommended?
No matter what the species is, this applies to all the food bowls for every single dog and cat. There is no danger to washing the bowl every 12 hrs. The only danger of doing that is leaving soap in the bowl.
No matter how thoroughly your cat or dog licks the food dish, it's not clean enough to use again without washing. That goes for water dishes, too. In some homes I've seen water dishes with the beginnings of algae colonies forming on the sides and the bottom. Who'd want to drink from that? Pick up your pet's food dish after every meal, then wash and scrub with hot water and soap. The water dish should get the same treatment on a daily basis. Better still, run them through the hottest cycle of the dishwasher to get them really clean and sterilized. From: http://www.vetstreet.com/our-pet-experts/spot-check-you-probably-arent-washing-your-cat-and-dogs-food-and-water-dishes-enough
Optimally, cleaning water and food bowls every day is the best – and if you’re feeding them wet food, you definitely should clean the bowls every day. If you are giving your pets dry food, PLEASE at least do a warm water rinse every day and clean the bowls with soap and water at least every few days.
There are several ways you can keep up with the cleaning. Most people will find using the dishwasher the easiest way to clean the bowls, but remember if the bowls are plastic to put them on the top part of the dishwasher to prevent melting. If you’re washing them by hand, use a mild detergent and warm/hot water. Rinse the bores thoroughly to make sure there is no soap residue left behind when you fill the bowls with water again because that could upset your pet’s stomach. From: https://petfriendsmagazine.wordpress.com/2013/02/27/keeping-your-pets-water-and-food-bowls-cleaned-should-be-part-of-your-daily-routine/
From what I've seen here in my research, my own experiences go along with this. I've done labs for instance I left the bowl out no cleaning and my dog got sick within 2 weeks. Another one I've done is when I wash it but leave soap in it. My dog didn't trust the bowl for 1 week.
Although there is no specific harm for washing dogs/cats bowls frequently, but there is definitely a reason why should we wash them.
I would suggest washing their bowls every single night. As I found that the smell of any leftover crumbs/layering on the bowls do attract crockroaches or flies; depending on what was contained in the bowl previously (dry or wet foods). These pests do carry germs/diseases that could infect our pets.
If you are worried about the chemical used in dishwasher, you can use homemade dishwashing liquid which can be make from natural enzymes.
Water goes stale if you leave it out. I've noticed that if I forget to clean the water bowl for a day, the amount of water the dog drinks from it (and subsequently 'makes up' from puddles when out) decreases.
Food bowl I've not noticed as much, but that I think is because we feed dry food topped with some wet. (Varies a bit what goes on top - some of what we're eating if it's suitable, sometimes a piece of fish, etc.).
But here too - it won't do any harm to clean regularly. If you use detergent, you'll need to make sure you properly rinse away the detergent.
My suggestion would be: fit a daily 'light' clean into the routine. Empty out the water bowl, quick scrub/rinse and same with food bowl. General aim is to alleviate 'staleness' in the water, and accumulation manky food.
And weekly do a 'deep' clean, e.g. dishwasher, soak in detergent, etc. Ensure as part of it you also do an extra rinse after, to ensure there's no lingering smells.