Certification

Admissions in IIM & top B-schools is strictly governed by CAT score (or other open test scores as required by the institute) along with minimum 50% at the graduation level. Certificate courses could only help at the time of campus placement as they would give you an advantage over other students.

The best way to learn CCNA is to setup your own lab either with physical devices or use a SIM tool. Lots of videos and materials are available online. Learning by practice is the best way to learn CCNA.

Yes, but the two courses should be from the same subject.

Hello,
You can take courses in e-commerce, Tally, advanced excel, power point presentation and other management related computer courses offered by several institutions.

It is excellent to see your eagerness in learning Java. Java is a great step towards CS. For a certification course, I would highly recommend the OCAJP or the Oracle Java Associate available for both Java SE7 and Java SE8.
For study material, you can first go through The Complete Reference written by Herbert Schildt.
Hub4Tech is the best institute for Java training.