Understanding the Right to Employment
The Constitution provides a fundamental right to employment. This does not mean you have a guaranteed right to be employed; rather, it means no one can stop you from seeking work and working for any person and any type of work. All fundamental rights are subject to duties and the reasonable control of the law. Therefore, the right to employment as a fundamental right is subject to it not being illegal.
Security Deposit and Employment Rights
How does taking a security deposit fit into this? By asking for and taking a security deposit, the employer is not restricting the right of the employee to work. The employee has the full right to seek employment elsewhere. He is also not, by this demand for a security deposit, being prevented from doing any work with anyone else. He is free to refuse this work and work for anyone else.
However, if he does agree to work, he is agreeing to the terms of employment, one of which is a security deposit and probably a reasonable notice period. It will be illegal for the employer to refuse to return the deposit if the employee fulfills the terms of employment and resigns with a full notice period. But the act of asking for and taking a deposit is not a violation of fundamental rights.
Legal Considerations
In terms of illegality, it would probably violate the Indian Contract Act (if you consider a job as a contract of service) on account of the doctrine of undue influence. But whether that defense works or not depends on how the lawyer presents it. In the current example, the defense of undue influence is of little practical use.
Personal Stance on Security Deposits
One last clarification: I am against the concept of a security deposit and things like keeping original certificates. But the question was about the legality of a security deposit, not whether I support it.
(Kargaonkar, if this is still not clear, drop me a mail; I will delete both the posts ;) )