Neither tunnel=culvert nor tunnel=flooded implies that you can walk through the object, that is your major misunderstanding. I would say that "flooded" even pretty much implies that you can NOT walk through the object because it is flooded with water. But even with "culvert", that follows from the tagging as a waterway.

The water surely enters somewhere and exits somewhere, but nothing in the tunnel tag implies that those entrances are usable by humans.

People doing dangerous things due to OSM tagging is an issue we have in the mountains with "footways" that are really alpine climbing paths. I have never heard of it ever having been an issue with tunneled water canals, at least here in Austria.