Married in secret, can marital status in passport be changed at a later date?

TL;DR. Don't lie on your application. It is usually much easier to hide info from or convince your family than the government. He should tell the truth on the passport application and take measures to hide the original passport from his family (Show them a copy with spouse name blanked out maybe). Or on the other extreme, if that is not possible and he feels marriage must be concealed at all costs, he may consider putting off the process of obtaining passport till the time is right.

There are multiple questions here and I'll try to answer the easiest ones first

Can marital status be changed discreetly?

No. Indian passports have spouse name in biodata page. If you declare your marital status, the last page of passport will have your spouse name. If your friend's family sees the passport, they will know the truth.

Can marital status be changed? With what documents?

Yes. If you need to change the status during application just mention it to the person on the counter. If you have a passport, apply for reissue of passport on account of change in personal particulars.

In the past, a marriage certificate was required, but it seems this requirement has been done away with. It is possible officials may insist on the certificate.

Be aware that if your friend mentions his status as single and later applies to re-issue passport with updated status, an observant officer may notice that date on the certificate is earlier than date of issue of existing passport and then fine him/stall his application on account of deception.

Will mentioning wrong status be a problem for him?

Yes. General advice given here is to not lie knowingly during application. Apart from the problem of explaining change in status in subsequent passport, your friend may face some uncomfortable questions from a foreign consulate if he plans for his wife to join him in a foreign country later. He will be required to disclose his marital status on most visa applications as well. If he lies there too and his lie is subsequently discovered, consequences can be severe.

It may make it harder for them to obtain documentation for children later if they don't have spouse names on passport ( e.g. India requires (Q6 in the FAQ) both parents to be present for minor child's passport or copies of both parent's passport with spouse name added).

During the verification process cops visit the applicant's home and they verify information provided from neighbor's as well. They don't ask about everything though but, if they find something odd they will question. Generally they just want to check whether the applicant is really a resident and Indian national.

It will lead to cancellation of the application and police may charge the applicant for providing false information.

FAQ Q2: Why is Police Verification required for issuance of passport?

A: Passport is a very valuable document. Thus, in order to ensure that it does not go in wrong hands, police verification is required for issuance of passport.

Source: https://portal1.passportindia.gov.in/AppOnlineProject/online/faqPoliceVerification

In addition to this applicant will also need to go to police station for interview and submitting the documents.