The Linux Mint comparison is very useful because it rules out several possibilities.
If the same hardware and the same VeraCrypt volume can open a directory with 25,000 images in about 10 seconds under Nemo, but GhostBSD takes several minutes with both ZFS and the VeraCrypt drive, then the storage itself is probably not the limiting factor.
I'd still be interested in seeing the dirperf report once the file operations finish. In particular, if the report shows that plain directory enumeration is fast but Caja is still slow, that would point toward thumbnail generation, MIME detection, filesystem monitoring, or another desktop-layer component rather than the filesystem.
It would also be helpful to compare these after the system becomes idle:
time ls -f >/dev/null
time find . -maxdepth 1 >/dev/null
If those complete in a few seconds while Caja still takes minutes, then we can largely rule out ZFS and focus on the MATE/Caja stack instead.