yes, VMFS 3.46 does have support of VAAI primitives.
My upgraded VMFS-5 does not have a 1MB block size. Why?
Upgraded VMFS-5 partitions will retain the partition characteristics of the original VMFS-3 datastore, including file block-size, sub-block size of 64K, etc. To take full advantage of all the benefits of VMFS-5, migrate the virtual machines to another datastore(s), delete the existing datastore, and re-create it using VMFS-5.
Note: Increasing the size of an upgraded VMFS datastore beyond 2TB changes the partition type from MBR to GPT. However, all other features/characteristics continue to remain same.
In short: If upgrade is the only option for you, then you won't get all the advantages of new filesystem.
VMware KB: Frequently Asked Questions for vStorage APIs for Array Integration