I think these two districts are in a quite bad spot right now. The market suffer from basically no terrain produce money and the market have weak adjacency, +2 when maker's and research quarters reach +5 in industrial era. Agarian district also have weak adjacency but atleast there is alot of food to be exploited.

The harbor is in a strange situation, it is probably the only non emblematic district that have 1 per territory limit, it is great for food but not that good for money, even though the tooltip consider it a money district, maybe because of sea trade. Instead of improving the harbor money explotation from the sea I suggest the 

Sea Trade familiy improve the adjacency between harbour and markets with maybe +3 for each level. This mean at industrial era harbors would get 12 money for each adjacent market and markets would also get +9 money from the harbor. This would make costal territories the prime moneymakers, due to the powerful relationship with harbor and markets and overall make both districts more useful. Also the 1 per territory limit for harbors could be removed, but a rule could be that harbors can not be placed next to each other and increase their stability cost to -20 so the are more expensive given they are more powerful than other districts.

Maker's and science quarters have much higher yields than market. I think the main issue with market is really more about money itself which is directly tied into its own fame star.

With number of religious followers and sites being so strong on money generation, perhaps for good reason given how rich the Vatican is / was, it still makes no sense to really build these merchant quarters imho. Only relatively late game when you run out of things to build, they can be popped out. I quite like the idea of strengthening the adjacency angle of merchant quarter and harbors. Reminds me of London's Cheapside.    

Religion have been changed/nerfed. Right now if you play as a merchant culture, you are better of building maker's or research quarters and use the ability to convert industry and science into money.