Can the main disconnect switches in an electrical room have separate locks on them

Residential or commercial ?

Commercial

Of course, and there is no difference between residential, commercial, or industrial.

The main disconnect and other panel disconnects are in a locked separate electrical room.
Is there a code requirement for locks on each disconnect switch? That is the real question.

I gave you a real answer to your first question.

There is no code requirement that they be locked, or that there be different keys.

The locking provisions are on disconnects for two reasons,

#1. Primarily to provide a means of locking Off if someone is working on the system downstream.

#2. To prevent shutting off a critical feeder by accident or intentially.


If this answer is not sufficient, need more details or explanation of your question.

Your answer is very logical.
I had an inspection and the inspector sited me for not
Having individual locks on the disconnects in the locked
Panel room. I cannot find anything in NFPA 70 or the NYC
Code that speaks to the issue. Maybe I just do not know where to look?

Best would be to ask the inspector for the exact Code he is citing that your apparently violating.

Could be a local housing code or requirement, for example.