There are hints in the LTSP docs that it is using SSHFS by default (instead of NFS) for sharing user accounts with the clients:
This makes sense because it is more secure than NFS, and maybe has other nice features as well.
However I think that DebianEdu is using NFS instead (correct me if I am wrong). Would it be too difficult to switch to SSHFS? This might be a nice "Google Summer of Code" project.
Even better would be to use the Coda File System:
It is a caching filesystem and would be very useful for Workstations and Roaming Workstations, to reduce the network traffic and to allow offline working (when the network is not working, or when you are outside the school network).
It is supported by the Linux kernel (maybe it needs to be enabled), but the problem is that it does not seem to be packaged by Debian (the laptops need a client that is called Venus). Also I cannot find any recent articles that show how to use it.