Hi,
These files comes either from your template or were added when you created view overrides in order to customize the pages of HikaShop.
Deactivating a file there means that you'll loose the look and feel that you added or that your template provider added, and instead you'll see the default look that is in HikaShop.
When you have a view override, it's possible that it breaks at each update based on what we change in the update. We try as much as possible to not change too much but we can't prevent all the different possibilities that could happen (or we wouldn't change anything ever).
So it's a trade-off: either you keep the template look and you test the changes when you update HikaShop to make sure it still works, or you keep the default views and it will work automatically after the updates.