You either need to get rid of villages spawning at the bottom of the world (i.e., not on islands), or move the vertical spawn coordinate of structures up 2 blocks. The village structures all lack the bottom 2 blocks, and thus are floor-less houses without chests and crops without soil beneath them. It might be fun for a player to use water or gravel to go down to these to interact with the surviving villagers and loot the chests and crops, but as is they are merely a curiosity and waste of time for our gentle player.