We asked one of the World Showcase lagoon boat drivers once. I wish I remembered everything he said.
All I remember is that it was taken out (either proactively or after damage - don't remember) durring the fall hurricane season of 2004, and it was put back in about a year later.
There was some interesting fact about the boat - I think my pregnancy hormones are blocking the memories from getting to my brain. Sorry!
We'll be in Epcot on Thursday - I'll have to ask again!
There was a CM at the American Dream who told me a nice long history of the Golden Dream. He mentioned the hurricane damage and how they weren't sure if the boat would be back. But Disney eventually decided to spend the money on repairs and they had a nice little ceremony to welcome the boat back. He also explained how you used to really be able to see the boat before they put the roof on the amphitheatre. One other thing he mentioned was that the Golden Dream really isn't a "real boat" , it's got alot of styrofoam in it.