Hi,
HikaShop doesn't change anything in MijoShop. When you do the import, HikaShop just gets the data from the database inside its own tables. It also tell you that you can use the redirect plugin to redirect the product URLs from MijoShop to HikaShop.
If you activated it, deactivating it will allow you to access again the MijoShop product page links.
That's it.
There is no reason the import would have changed that "shop" menu item, so not much we can help with since I suppose this is a MijoShop menu item. I would recommend to check the settings of that menu item with the support of MijoShop.