I would assume that you use zfs there. It requires tuning to work normally, like a record size for example.
See Topics tagged zfs, and Notes on storage node performance optimization on ZFS in particular.
I hope @arrogantrabbit or @SGC can give you more advices how to tune it.
Usually your system could struggle with disks subsystem, when there are some issues, may be even with disks or hardware. It should not hangs on filescans, especially so tiny ones (it traverse only across the trash, not blobs).
If your system cannot deal with a few GB of files on disks, it doesn’t sounds right.