1. While installing OVA where should I need to install it? Does it the destination dedupe store say 3.02TB as above and it can be any small LUN other than dedupe store.
It should be deployed within the vCenter (The vCenter in which the VMs to be protected exist). You can always start with Thin provisioning if you do not have 3.02 TB of space.
Refer this blog article for quick deployment & configuration - http://onevirtual.wordpress.com/2013/11/15/vdpvsphere-data-protection-5-5-deploy-configure-quick-start/
2. In case if it is other than de-dupe store how will this is going to be added to ova appliance.
You have an option to choose multiple datastores while configuration - The above article should cover that information too.
3. As NAS box for dedupe going to be present on production network and will be accessible via production network only.Does it make any performance issue?
Check if you can take advantage of hot-add instead of backup over network.