hi,
you can upgrade the vcenter to 5.5 and then upgrade the desired hosts to ESXi 5.5 an dcontinue with the same datastores with VMFS 3 (WHich will still have block size 1mb, 2MB, 4mB and 8MB). Do not upgrade Virtual machine hardware version to 8 let them be still on 7. The reason is you can use vmotion between ESX 4.1 and ESXi5 when needed.
Later on when you decide to upgrade other hosts to ESXi 5.5 go-ahead and upgrade them. Then upgrade the datastore File system to 5 which gives you uniform block sizes also u get 64 TB single largest datastores (If required). Then upgrade you VM Hardware Version and tools.