I've heard of the calcification of organs, and of hypervitaminosis. Vitamin A has been particularly implicated in causing problems, which is why many supplements have switched to using Beta Carotene as the source for vitamin A. It is apparently much less likely to cause problems. The fact that the information regarding negative effects of supplements is so scant, as you pointed out, does make the balancing act difficult.
I have to admit that I used to be like you. I scoffed at the supplements, and my turtles suffered because of it. I got strange, uneven, and slow growth until I finally put the turtles outdoors at about 3 inches. Now, with the combination of lighting and supplementation, I get better growth indoors than out. I also have less "failure to thrives" ,a.k.a. less hatchlings die.
I should be more specific. I don't supplement EVERY feeding after one month of age. From hatchling to one month, I only offer live feeders. I offer them either every day or every other day, depending on how busy I am. I alternate dusting with calcium and multivitamin at each feeding. Then, I add in some non-living items at one month of age. I soak Reptomin until it's soupy. Then I mix in extremely finely chopped kale and turnip greens at a ration of 2 greens to 1 Reptomin by volume. Then, I roll it into little balls, freeze them on wax paper, bag 'em up, and thaw them as needed. Lately, I haven't been adding any supplements to that concoction, since they've altered the recipe. They get this about once weekly. Then, twice weekly, they get tomatoes, squash, sweet potatoes, greens, cucumber, and tons of other veggies as I find them in my fridge. So, really, my turtles are only getting dusted feeders two to three times per week. I still alternate between calcium and multivitamin on the feeders. I've also been experimenting with liquid calcium and vitamin supplements, and I like their ease of use so far. But, it's six of one and half a dozen of another. The purpose of this paragraph is not to tell you what to do, but merely to illustrate that I don't stick a funnel in the turtles' mouths and pour vitamins into them.
Casi...you once indicated that you don't give your eggs or hatchlings any special care. You seemed to state that you maintain your box turtles in outdoor pens, and leave the hatchlings to fight for themselves. Is this still correct? I'm not saying that it's wrong...it's probably a better way of ensuring that you raise the "fittest" hatchlings, but it could be the reason why you don't have to supplement. Once mine go outdoors, with the exception of gravid females, I don't supplement more than once a month at most.
The reason that we have to supplement is not only because we can't offer the variety of food items available outdoors, but also because our feeders are most commonly gutloaded with only one thing...potatoes. If you can catch live insects outdoors in a pesticide free environment, or gut-load your insects with really high quality and varied vegetation, supplementation becomes less necessary.
For what it's worth, I have one caveat...I've been injection the liquid supplements into earthworms before I offer them to my aquatics. I've noticed that if I overdo it, they will go off of feeding for several days. It appears as if they have a "stomach ache". I've stopped doing this altogether, as it made me nervous. That's what I get for trying to fix a problem that didn't exist, as I've never had a problem with growth and health in my aquatics. Box turtles are another story.
Sorry for the long and boring post.