1-is there any issue if I upgrade while the disks are online or I should disable them.
The upgrade should not harm the LUNs in any way, so there's no requirement to unpresent/unzone the storage for the upgrade.
2- Is there any points should I consider before upgrading from ESX TO ESXI.
Ensure compatibility of all components (hosts, HBAs, storage, firmware, ...)
Ensure that any add-on's you installed - especially in the ESX host's Service Console - are available for ESXi 5.0. What I am thinking of are e.g. backup applications.
Upgrade vCenter Server (unless already done) before upgrading the hosts.
André