I found an interesting article about the public battle waged by Imagineers to keep the subs open, and Paul Pressler who complained that the subs took up too much, "storage space".
Back from the depths - Los Angeles Times
Marty Sklar hired a naval engineering firm to look at subs and they said they had 40 to 50 years of life left in them. (You'll see why he might have done this as the couch potatoes in Maintenance at WDW made up stories so that they'd have to do less work!)
One website says that the 20,000 sub ride in WDW was closed when Eisner asked for savings cuts, and maintenance workers hated the ride so they took advantage of the situation to save some money and not have to hassle with maintenance. Then even went to far as to pull a fast one on Michael Ovitz by making the ride look like it was unsafe and on the verge of falling apart.
20,000 Leagues Into The Toilet by ED Tucker *** A Crazed Fanboy Presentation
Here are some interesting Jim Hill articles,
What actually became of 20K's submarines: Part I
What actually became of 20K's submarines: Part II
Jim Hill said that subs in Magic Kingdom had to be shut-down for three months of the year, and hence was a maintenance nightmare. How long do Disneyland's subs go down for? Certainly not that long? I know that they use special glass-based pigments which will make the colors last much longer, thus requiring less maintenance.