There are two primary disadvantages to disk or directory encryption. The first is probably the most serious; if the password is forgotten, the data is permanently lost and completely unrecoverable unless unencrypted backups (or encrypted backups where the password has not been lost) are available. The second disadvantage is performance. Most software encryption modules perform well, but there is no avoiding some overhead, even if it is minimal. Hardware encryption, such as that provided by the motherboard or the disk controller or drive itself, generally does not have significant overhead.
Best practice is to evaluate whether the disadvantages of encryption outweigh the potential damage from compromised or stolen systems.
Most corporate policies require partial or full (if available) disk encryption on laptops, and directory encryption as a minimum on public servers.
