yea... there is no telling what did it... And I dont remember spikes on the nucleus, just on the walls. the nucleus just controled the fluid and it did damage holding you, then throwing you into the spikes on the walls.
The cuts in the tree are there as a kid, after going back and looking and noticing the only boss that has claws like this are King Dodongo, and Volvagia, and I highly doubt either of the fire bosses were at a lake. With this I'd have to guess the cut was put there during the war that was in hyrule before the king unified the land. Because I'm sure someone else read that the Great Deku Tree, said that "There was a war and links mother was dieing and the Dreat Duke Tree seeing that this was a child of destiny took in link. So I'm guessing that the cut happend during the war being mentioned right there. But really the only reason it's there is because a developer wanted to see who would still be talking about a cut in a tree, after what is it 12 years now? from the time the game was made? I didn't check to see what time this was posted. But if it came out in 1998 and it's now 2010. So I'm sure there's some developer somewhere reading this going.. "Wow this kids played this way to many times to know that...." It wasn't until my 17th time through I noticed the cut >.<