Criteria for replacing rusty roof screws

The majority of screws on our 15 year old colour bond roof have red/brown rust on them. The sheet metal is not rusted and it is confined to the screw head. Perhaps the socket damaged the colorbond coating on the screw head during installation.
Water based painting contractors didn’t seem to address the issue when quoting but now a contractor says the screws should be replaced with thicker screws. This seems a bit of an overkill to me.
So the questions are,
Can a water based paint system kill the rust effectively? And what criteria would would define the adequacy of painting the existing screws compared to replacing them please?

You will be far better suited to replace the screws. The fact of the matter is that the screws have a wear item on them in the gasket. I don't think you will get effective rust abatement with just painting them vs. replacing them.