There are no significant on-disk format changes going from version 3.33 to 3.46. However, there is a significant change between VMFS driver version 3.46 and driver version 3.33. In particular, 3.46 contains VAAI extensions, which leads VMFS to use hardware accelerated locking and the hardware accelerated data mover on VAAI compliant hardware.
So the short answer is that you do not need to upgrade to a new on-disk vmfs 3.46 but instead the new 3.46 driver on ESX 4.1 will bring you the benefit even with vmfs 3.33 on-disk filesystem, if these are on array whose firmware is upgraded that provides such VAAI extensions.
VMware ESX 3 – VMFS ver 3.21
VMware ESX 3.5 – VMFS ver 3.31
VMware vSphere 4 – VMFS ver 3.33
VMware vSphere 4.1 – VMFS ver 3.46
VMware vSphere 5 – VMFS ver 5