Answer to your first query on linux vCenter :
vCenter Server Appliance: Linux VC capability
Hosts (with embedded vPostgres database) 100
Virtual machines (with embedded vPostgres database) 3000
Hosts (with Oracle database) 1000
Virtual machines (with Oracle database) 10000
Ref:http://www.vmware.com/pdf/vsphere5/r55/vsphere-55-configuration-maximums.pdf
If you install new vCenter from scratch ie. 5.x. you can add your ESXi 4.1 host to it but you will lose all vCenter settings/configuration from earlier vCenter.
You need to configure everything from scratch on new VC