The VMFS partition is just one of multiple partitions on the disk/volume. Running fdisk -lu will show you the partitions. Deleting the datastore and recreating it with another block size is comparable with re-formatting e.g. the D: drive on a Windows host, which doesn't affect the C: drive/partition either.
Take a look at http://rickardnobel.se/esxi-5-0-partitions/ (although for ESXi 5) to see how the partitions look like.
André