Illness originally was introduced much later on in the WN, though she was sort of hinted at prior. Manga follows the LN closer, where Illness appeared much earlier. She also showed up for a single panel at chapter 7 pg 8.
Now hold on a mo, boy, your tunnel does explain the water in the basement, but you only completed that a year ago. Noises have been going on for a decade, something doesn't add up.
2 should be from Read Danshi Kinsei Game Sekai de Ore ga Yaru Beki Yuiitsu no Koto: Yuri no Aida ni Hasamaru Otoko Toshite Tensei Shite Shimaimashita for free on MangaDex...
From the spoilers I read on that manga's final chapter, Axe-kun did us a huge favour with how much of a mess the story became from that point, and that's putting it kindly.
If my memory serves me right, the island and inland sea was mentioned to be filled with monsters in the WN/LN, so it wasn't as if there was a vibrant shipping economy in the area to start with.