Squids make ink. I wonder if it is edible? Squids are edible. ROFL
I'm guessing the "edible black ink" is used as a colorant, not an active ingredient. After all, what color should charcoal be? If by making it medicinal it comes out gray, then people might think something's wrong with it and won't use it, so the manufacturers color it up a bit. A lot of our food is colored because of our preconceived notions about what colors things should be, not because it has or needs color. I get some spicy crab dip a lot that is tinted pinky-orange. When I made some from the same ingredient list at home (minus the food coloring), it came out kind of gray (because of the dark crab meat). So either people think that's not an appealing dip color, or they want the pinky-orange color to make it look spicy. You don't imagine gray dip to have cajun spices in it, do you? Cajun spices make food red... or so we think.
Since you bought them, go ahead and try them. If they relieve your gas, then you know they work, regardless of what color they may or may not make your poop. Would you be more willing to try them if instead of "edible black ink" it said "Black #35"? All food dyes boil down to the same thing, really.