Jason over at Disneygeek.com has a whole section on the 2003 draining with great pics. AI recommend you check it out as he got some great shots. They're under the construction progress section I think.
From what I know... The draining of the river is not so much for Fantasmic! As it is to do some work on the Mark Twain and Columbia guide rails.
Probably some repair and maintenance on the fountains for the show, and gas lines too... But I doubt they will be replaced with moving nozzle designs. Moving nozzles could be installed on the fountain lifts without the river even being drained. Each fountain lift can rise much higher than they do for Fantasmic! They can get a good 2 feet above the water level for work on the entire structure.