1)will there be any impact if i change the owner of the Job to the same as the service account on which the SQL agent is running?Depends. What kind of permission the SQL Agent account has? It has access and it's able to create files in the backup location?
2)After i change the owner to other name(preferably the service account of sql agent), will it create any issue in future if the SA login is disabled?Why do you need to disable the SA account? Do you have any other user with similar permission?
Yes the SQL server Agent account has all the required permissions.Then you should not have any issue by changing the job owner.
Also client and security team is much concerned about the SA logins as its a big threat for the hackers(as per their views).Change the password to a strong one or permit only Windows Authentication to the SQL Server instance.
Now my question is "Is 'SA' should be the database owner for all the system databases? Is it a recommended practise or something else to consider ?Yes if you have SQL Server Mixed Authentication enabled.