Encryption of Time Machine backup disk taking several days
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).