Deep running is a feature of H.sie's patch to sh3.exe, which is included in many mega-mods. It is meant to simulate various torpedo running failures.
The H.sie mod installation is easy to mess up, I understand especially on Windows 11. Don't ask me - I run Linux which lets me do what I want
Search for the file Readme_V16B1.pdf Read the pdf and be enlightened.
Early war attacks in rough weather become extremely challenging. H.sie's options selector can be used to turn it off, although the game is much better with it on IMHO.