It is possible and supported to upgrade ESX 4.x to ESXi 5.x, so you shouldn't need to have to reconfigure anything, but personally I'd consider a clean reinstallation to avoid any confusion in the future regarding e.g. partitioning, ... At the time you reinstall/upgrade the hosts, I recommend you also upgrade the host's firmware.
I don't know the size of your environment, and whether a complete reinstallation of the hosts (which would require configuration) would be a way to go!?
André