I believe this is related to how the "pool" actually forms. If I understand it correctly, drivepool reads the disk before the diskencryptor application (eg doesn't read through the program to get to the file system, it ties directly into the OS Kernel to read the NTFS / volume mounts directly). It then forms a synthetic disk over top of your real disk and a "fake" NTFS based volume while utilizing the underlying drive's file system.
A possible work around is to use clouddrive's local disk provider, although it has it's own encryption. Clouddrive doesn't make a "fake" disk like drivepool does, and I believe this can work on a local disk + encryption software. If you were to create those drive it could be included in a pool and you could use that.
@Christopher (Drashna) <--- this guy knows more and might be able to correct my assumptions.