This test looks at the total amount of antioxidants found in chocolate chip cookies. For the food sample used, it was an unspecified store brand purchased somewhere in the United States (they don't disclose where). Obviously a baked good such as this can be made any number of ways, some much healthier than others. Even though we don't have the specs on where and how this was made, it's probably a good average to use for gauging the nutritional value of chocolate chip cookies.
The good news is that they do have a moderate amount of antioxidants, at least for a processed baked product. Then are chocolate chip cookies healthy? That would be a stretch to say the least. Even if they are vegan, gluten free, non-GMO, and whatever else you want, it wouldn't change the fact they are loaded with sugar as well as carbs.
If you want to make your cookies healthier (not "healthy" but just less bad) then one easy way to do that is to use lots chocolate chips made from unrefined or lightly processed chocolate. Choosing the lower sugar varieties (i.e. dark chocolate) are idea. That's because raw cocoa is an insanely rich source of antioxidant content.
Other easy ways are reducing the salt you add, so it's lower sodium, which will make them a more heart healthy recipe. Perhaps the best nutritional boost would be using better flours. Whole wheat is an improvement since it's lower glycemic (and therefore better for diabetics) but if you really want to kick it up a notch, try sorghum bran, which is a more nutrient-dense gluten free grain. If you're on a plant-based diet, vegan butter substitutes like Earth Balance spread could be used, as well as non-dairy almond or flax milk. Flax meal or chia can serve as an egg substitute.
Research Support, Non-U.S. Gov't: Carlsen MH, Halvorsen BL, Holte K, et al. Nutrition Journal NIH Jan 2010