1. It's two darn different temples! Just because it was six temples in the first game dosen't mean it have to be the six exact temples in all the other games. I don't think that have ever happened, actually. They have nothing to do with the six temples that anyway lies on the bottom of the sea...
Have it ever occured to you that Hyrule in WW is FLOODED? Heck, it dosen't even take place in Hyrule, Hyrule is the land on the BOTTOM of the Great Sea. Of course it dosen't have as many Temples, it's a whole new world!