On NTFS partition with 64KB cluster size it takes very long for CCleaner to wipe MFT (I'm not talking about wiping free space!). Remaining time is slowly increasing instead of going down and HDD actuator is grinding like crazy if I can say so. After 1,5 hour it only completed 17% and current remaining time is 1h 20min and slowly increasing. My MFT size is not that big, 258,50 MB with 264703 entries (and it's not fragmented). I'm pretty sure the problem is 64KB cluster size.
As far as I know there's no way of wiping the MFT without also wiping free space. Do you mean the Wipe MFT component of Drive Wiper, or what? If so then the notice that Wipe MFT has completed may not necessarily coincide with the actual event.
Wipe MFT fills the MFT by allocating enough small files to fill it (and overwrite what was there before) and then deleting them. This is a NTFS heavy process. I can't see that the cluster size would have much, if any, affect, except by reducing he number of I/Os required.
I'm talking about "Drive Wiper -> Free Space Only". It's done in two steps. First, as you said, it allocates large number of small files and directories with "...ZZZ..." filenames, second it creates one big file filed with zeros to wipe free space. Now, I'm talking about first step here. It's this that takes very long to complete. And I know how long it takes depends on number of entries that are marked as deleted in MFT. And it's not a heavy I/O process because using simple batch file to create 100000 files took a few seconds to run.