Encryption of Time Machine backup disk taking several days
It has been two days since I started Time Machine encrypting my external hard drive (6 TB in size.)
Why is it so slow? (disk connected via USB 3)
When I selected the disk for Time Machine, Time Machine itself formatted it to Mac OS Extended (journaled, encrypted). It then ran a successful backup, after that it encrypts the disk - what logic is that? Did it first write the files unencrypted, then it encrypts the files? Really?
Regarding your first question, it is hard to say exactly "why" it is slow. There's multiple factors involved - obviously reading in and writing out 6 TB of data from an external hard drive is going to take some time. If we say your drive does 100 MB/s (which might be very optimistic for some drives if we're looking at small transfers), then that alone takes approx. 18 hours.
Add to that the time needed to encrypt and validate the data as well as overhead. I doubt that the process is optimized for taking the shortest time - rather it is optimized to affect the rest of the system the least, so that you can keep working on your computer while it runs.
Regarding your second question: No, it does not first write the files unencrypted and then encrypts them afterwards. The files are written to disk in encrypted form. However, you should note that when you encrypt the drive, you're not only encrypting the files you transfer to it right now, but all the blocks on the drive (used or non-used for your data).