If you do it properly, no there are no health issues.
A combination of two things are required to kill beasties: heat and time. The higher the heat you expose them to, the faster they die. Generally any temperature above 130 F is enough to kill most beasties, it just requires a significantly larger amount of time compared to a higher temperature.
I go into a lot of detail regarding Salmonella in this answer of mine:
Is it safe to eat a cooked steak that (briefly) touched the plate that was holding the raw meat?
I have several tables there to show exact timings, etc.
If you think I should copy/paste that here, then let me know in a comment
In my experience, whether or not you peel a fruit or vegetable has more to do with how easy it is to digest than any level of toxins. If you're going into the realm of herbs, however, then you need to be more careful, as some are quite potent. But as long as we're sticking to fruits and veggies, here's my advice, and it's pretty simple:
Clearly things like melons, and corn don't have edible peels, simply because their outer layer is too difficult for us to masticate, and then digest... Things like citrus peels can be digested, but not when they're raw. They need to be pickled, cooked (think of marmalade) or turned into a zest. When it comes to soft, thin peels, like apples, pears and kiwi, it's more of a personal preference. Some don't like the feel of a furry kiwi slice going down, but I don't mind it, so I slice it right into my cereal.
In the realm of veggies... Yes, stems are great for you. If it's really difficult to chew it, it's not going to be broken down enough for your stomach to handle it, and extract anything useful from it. Ex: Broccoli stems - they'll benefit even from some light steaming, and they're GREAT for you. But raw? Rather difficult. The florets however are a classic raw snack. That's my general guideline. Same with artichokes. They need some kind of cooking in order to be digested. But carrots? Kale? Celery? Simple chewing pulls them apart enough to make the extraction of nutrients easy for the body.
Hope that helps!
Mindy
P.S. A great tip for raw kale - not everyone likes the consistency of raw kale because you have to chew it for soooo long. BUT, if you massage it with a bit of lemon juice, and a touch of olive oil until it softens, and the color brightens (5 minutes or less), it's easier to chew, very tasty, and you haven't cooked any of the nutrients out of it!
Best Answer
While I agree that these types of warnings are conservative and partially CYA, I would suggest that they not be dismissed.
What needs to be understood is that there are other factors involved past the production method. Even if a mfr./producer observes and maintains the highest quality standards in their production facility, they have no control over how the food products are handled after leaving their facilities.
There are many transportation and storage steps between the time products leave a production facility and the time you pick it up from a grocer's shelf. If, in any one of these steps, the food has not been handled properly, the safety has been compromised.
While I would say that the risk may be minimal, it still exists. I am not overly conservative in my own kitchen, but one needs to know that the risk can be real. And just because something hasn't happened yet, it doesn't mean that it can't.