Provided drive encryption operates at something below user level (which seems to be the case for most whole disk encryption products) there should be no issue backing up encrypted disks.
When user-level file systems are encrypted with credentials that aren't readily available, you might experience some issues. In a whole disk encryption deployment, the standard file system should be available to running processes (the encryption happens “under the covers” when data is written to disk).
CrashPlan PRO supports Windows EFS. Here are instructions on how to use it.
CrashPlan PRO has full FileVault support. Just make sure that when you install CrashPlan PRO you install as the user who owns the FileVault account. Backup will occur only when you're logged into the computer, as that is the only time CrashPlan PRO will be able to see individual files. We support a single FileVault per computer.
There is an option in Truecrypt enabled by default called preserve timestamps of file containers. When enabled, Truecrypt retains the file timestamp from initial file creation. Essentially, it looks like the file has never changed and CrashPlan PRO won't back up the changes. If you disable this option, the file timestamp changes when files are modified, which allows CrashPlan PRO to back up the changes.
If you're using another disk encryption product with CrashPlan PRO and have questions or would like to share your knowledge or discuss, please visit our User Forums.