I think it has a lot more to do with the sheer amount of sea trade passing through that area and it's supposed to motivate them to open their border to get advantages from trade. That said, the amount of ships passsing through is probably not the best indicator for that.
Maybe something on the lines of:
Sea trade routes to and from Indonesia (in it's core?) give and extra 100% yield. Extra food per foreign trade route or % trade route yield in food.
But that only takes into account the trade going into Indonesia and not through Indonesia, and dilutes the advantage that's supposed to come from the control of the south china sea and the strait of singapur through all the cities, not to mention that extra movement in ocean tiles also reduces it's strategic importance.
All said, maybe someone has a better idea

You could also have something on the lines of:
The Indonesian Capital gets extra gold/commerce for the population in Indian, Southeast Asian, Chinese, Korean and Japanese coastal cities, to reflect it's importance as the region trade hub.
That said, I don't know if any change is needed.