Since other resources scale (yields), I've considered scaling happiness from monopolies a bit. Not sure about it, though, as happiness values in CBP don't inflate quite as bad as vanilla.
I agree with you, this is not really a good solution.
The problem is that the 3 happiness monopoly bonus isn't really good at any part of the game, it is not like you ever think 'Man, I wish I got +3 happiness instead of +20% growth or 25% GAD'.
I can think of three semi-easy solutions one of them is pretty boring and the other one is a clear power-creep. These suggestions are both outside of the building changes that I'm going to suggest later on.
1. Remove most of the +3 happiness monopolies and replace them with better ones, leave the Indonesian ones and both the camp luxuries (You could also keep one of the plantation ones, but then you'd need to bump up the base-yields of that resource quite a bit probably). Bump up the +3 happiness to maybe +4 or +5 because honestly, +3 is just not enough.
2. Scrap the entire +3 happiness monopoly, redistribute the remaining luxuries into other monopolies. Add some happiness (between 0 and 3) to the other existing monopoly-bonuses, for example the +3 gold monopoly (being one of the weaker ones) could get +3 happiness while +3 food monopoly (being one of the stronger) could get +1. This would allow for some balancing between the monopolies but it is clearly a powercreep.
3. Combine the +3 happiness and +3 gold monopolies into one, make those monopolies add maybe +2 gold to tiles and +3 happiness globally.
Building changes.
I don't know quite how possible this is (maybe the buildings can only have that many bonuses?), but could we please consider moving the medieval/renaissance era building bonuses to ancient/classical.
By that I mean moving the bonuses to gold/silver/gems from banks, the bonus to Ivory from a circus and the bonuses to Tea/Coffee/Tobacco from the grocer to ancient/classical era buildings.
Yes this is going to create a lot less difference between luxuries, and to some degree diminish the whole point of 'More Luxuries' but being stuck with tiles that only kick in halfway into the game while others kick in in ancient era is painful.
You could still have some form of scaling involved, you could have some renaissance or industrial era building adding +1 gold to all luxuries, at that point the gold wont really matter much but it is just a fun thing.
As for which resource to place where, most of the ones I suggested moving are considered trade-goods(duh), so splitting them between the market and the caravansary would probably make the most sense. Tobacco while clearly a trade-good could also fit into the temple, being a religious thing I suppose.