Provided I have a valid CA issued .cert file. Technically, how many keys a single .cert file can have? more than one public key? or only one public key
As said in comments, an X.509 certificate (RFC5280) contains exactly one public key. No more, no less.
For same subject, will CA issue more than one certificates?
CA may issue as many certificates to same entity as necessary. There are no limitations on the amount of issued certificates per subject.