I highly doubt the SeaCabs were removed-- DiveQuest divers have recently reported seeing them in the tunnel, and Disney wouldn't spend money ripping out a system until they knew its future.
Even so--- it doesn't matter whether the SeaCabs were removed. The vehicles/track will likely be redesigned before Nemo is installed.
There are two reasons they closed the SeaCabs:
1) The open-door design encouraged too many people to step out of the vehicle, triggering an automatic E-Stop.
2) It made little sense to spend money on staff and maintainence on a ride that lasted 2 minutes, going past the same visuals you could see upstairs.
Originally, the "undersea tunnels" was to be the climax of a much longer dark ride. To contain costs, the dark ride was replaced with the film-- while strangely retaining the seemingly pointless ride through the tunnels.
IF (and that's a big IF) Nemo is going to be a dark ride, Disney will hopefully expand the ride track through the current theater space--just as it was originally designed.
However, if budget-cutters prevail once again, I won't be too disappointed if The Living Seas gets a new film---- and the old ride "tunnel" is carpeted and turned into a walk-thru.
For more history about The Living Seas, check out:
http://www.intercot.com/edc/LivingSeas/lsconstr.html