Since Diskeeper doesn’t see the FancyCache as a separate storage device, the reads/writes that do occur from an application (defragmentation activity included) over to NTFS.sys will be processed according to the various storage drivers on the stack. I would agree when the accumulation of fragmentation over time results in a situation where if a defrag is performed, the data blocks stored in cache are subsequently flushed and replaced with more recently accessed data blocks then one could potentially see a short term negative effect on cache hit rates.
To solve this problem Diskeeper engineered a technology called IntelliWrite and that prevents the vast majority of fragmentation from occurring in the first place. By helping Windows (NTFS.sys) allocate a more appropriate amount of data in the first place, data is written contiguously in a more sequential rather than random fashion. This will improve cache hit rates and precludes the need for defragmentation after the fact. On average, IntelliWrite prevents 85% or more of the fragmentation without the need for file movement. As a result there are no wear and tear issues to speak. In fact, erase activity as well as the Write Amplification index on the SSD is greatly reduced and documented with the use of Diskeeper’s technologies.
I haven't played with CleaverCache is such a long time, I don't feel qualified to comment.