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I just received this mail from OmniFocus support -

Hi Puneet,

Thanks for taking the time to write us! I apologize for any confusion. If an action or project has a note assigned to it, the note will appear dark gray. Otherwise, it will not appear at all. It appears along with the flag a very dim gray when an action or project is moused over if no note exists, but otherwise if the note icon is there at all, it means that action or project has a note.

I have attached a screenshot clarifying this. Please let me know if you have any questions. Thank you very much for your help!

Sincerely,

Michaela M.
Support Ninja
The Omni Group

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So, it seems it was indeed my mistake. I didn't realize that the icon does not appear if there is no note. (all my test actions had notes). Apologies to the support team. Its people like me make their job tougher :). However, my other point still remains valid that there is no option in the menu to show/hide all notes within project.