Will there be any implications on the site's optimization efforts when my domain is set up in two servers : default and backup server?
Assuming the backup server will only come online when the default server is down, and both are configured to serve the same contents for the same domain, there should be no implications. The search engines only see the "external" part of your website (i.e. which requests it accepts and which responses it returns), they have no idea (or interest in knowing) how it's structured internally.
Given that your server configuration is "transparent" to search spiders, there should be no impact at all.