Hi Jennifer,
Unless things have changed, The Seas with Nemo and Friends is not opened during
Extra Magic Hours at Epcot. Here is a list of attractions that are open:
Morning:
Living with the Land, Mission: SPACE, Soarin', Spaceship Earth, Test Track
Evening:
All of the attractions that are open during the morning EMH, Captain EO, Journey Into Imagination with Figment, Gran Fiesta Tour Starring the Three Caballeros, Maelstrom, The American Adventure.
I believe that the character greeting spot has been open during Extra Magic Hours. The boat usually does continue to run; however, it's much quicker to walk from Epcot to your resort.
Hope this helps. Have a magical vacation!