The upgrade procedure from VMFS-3 to VMFS-5 will require downtime of that datastore?

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False:
http://kb.vmware.com/selfservice/microsites/search.do?cmd=displayKC&docType=kc&docTypeID=DT_KB_1_1&externalId=2003813

Upgrading from VMFS-3 to VMFS-5
Can I upgrade while my virtual machines are running?
Yes. Upgrading from VMFS-3 to VMFS-5 can be done on-the-fly (virtual machines do not need to be powered-off, suspended, or migrated).

Do I have to use the command-line to upgrade to VMFS-5?
The upgrade to from VMFS-3 to VMFS-5 can be done either via the ESXi 5.0 command-line or via vSphere Client.

Note: Ensure that all ESX hosts accessing the LUN are already on ESXi 5.0.

To upgrade to VMFS-5 using the vSphere Client, Under Configuration > Storage, highlight the desired VMFS-3 datastore, and click on Upgrade to VMFS-5…
To upgrade to VMFS-5 using the ESXi host command-line, use the command:
# vmkfstools -T /vmfs/volumes/

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.