For a company which issues shares, a signature is the only way to ensure that the person is the same individual to whom shares were originally issued.
The registrars have signature experts for matching signatures, but some companies also have an independent audit team which verifies the signatures of shareholders for demat and other requests.
Usually, when a signature mismatch occurs due to a difference in the spellings, company, registrars and DPs require the signature of the share certificate/account holder to be attested by his bank along with the seal of the bank, name of the bank manager and the address of the branch along with a self-attested copy of the identity/residence proof.
In case of a major difference in the signature, an affidavit from the court along with the identity/residence proof needs to be submitted.