Can I ask did you test this with action replay or with emulator and with cheats? If you have that kind of weird cheats what are rare with gameshark on cube. Can I get those too from you? You can PM me if you have any. Thanks for advance!
I used Dolphin's built-in Action Replay cheats, and modified them. It's not too hard, just find unencrypted codes that give you other items, let's say, the Hookshot. The unencrypted code would look like this:
003c4c57 0000002f
The 2f at the end of the code is the Hookshot's item number.
Now, looking at the unencrypted code that gives you Bottle 1 (003c4c52 00000050), you see that 50 is the ending two letters. If you put the 50 (or another item number, for different items, or different contents for the bottle) in place of the 2f for Hookshot, you'll get an Empty Bottle in that slot instead.
If you're going to be doing this on console, you're going to get to get a program to encrypt the codes (GCNCrypt, I believe). Also, if you're on PAL (which I assume you are), you're going to need to get codes specifically for the PAL version of Wind Waker. Of course, another problem arises if you have the later piece of shit version of Action Replay, that disallows the adding of codes, in which case, you cannot do anything.
Edit: Also, some things for Tower of Gods.
Scale Room:http://www.youtube.com/watch?v=_NVDAvfU9L4Boss Key, Leaf Method (easier than damage boost)http://www.youtube.com/watch?v=AAfHgNtoZ8sAlso, it is possible to shoot out both of Gohdan's eyes without him using his laser attack, but it's insanely luck based and requires manual aiming.