Interestingly, the hookshot is displayed on the save screen in the menu.
The hookshot occupies the same spot as the mercury vial in the inventory. So you do have the hookshot, but it's hidden by the second vial you're not supposed to have.
(I just fixed that bug, thanks again for letting me know!)
You can indeed edit the save file to remove the second vial. First, make sure to exit the game. Then open "save1.json" with a text editor. When you see
replaces it with
That should do the trick. The extra vial will be gone, and the hookshot will reappear in the inventory.
Sorry for the inconvenience! But thanks for reporting these bugs to me, it's really useful ;)