It is usually a "cleanliness" thing. If he is only doing it in the house then try to not react to it at all. Just get him outside ASAP. If he is having accidents in the house then you need to keep a better eye on him. Get him out more often, on leash, and praise him for going potty outside. The way to "break" him of it if he is doing it outside is to have him on leash to go potty. Talk to him while he is doing his buisness, trying to distract him from cleaning it up while not distracting him from his business.
It could be because he was in a shelter. Often they just don't get outside enough and learn to keep their sleeping area clean. Cleaning up after themselves becomes habit. They can also learn it from mom if she keeps cleaning up after them once they are weaned. It is natural for a mom to clean up after the pups. It starts at birth when they need to stimulate the pups to urinate and deficate by licking thier abdomens. It then continues while they are nursing so that mom can keep the "den" clean.
I have never had a dog drink their urine while going. I've had some that will do it with other dogs (as well as catching bms as they are produced ICK!). I have heard of it though. I'm not really sure what you can do about it. Like I said breaking of it is quite touchy while he is still house training. It is a fine line between discouraging his doing a gross behaviour and discouraging the appropriate behaviour of going potty outside.
As for whether it is healthy for him or not....I wouldn't worry about it. Urine is a sterile solution and should cause him no harm. Coprophagia (eating bms) is common in dogs actually. There are things you can do to make the fecal matter taste bad. Using MSG on the food seems to work well. Some people swear by pineapple or pumpking, my issue with those is that you need to feed so much that, for a pup especially, it can unbalance the diet.
I doubt it is a deficiency of some sort. Even the worst foods out there have all the "basic" nutrients they need. But, if he does have a biologial problem that stops the absorption of some nutrient then, it is possible.