Note: I havn't actually had a chance to play this yet, ive been going off of valk's decs on the first page, Hopefully I'll have a chance to actually play this weekend
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For no foreign trade civics:
I see no problems thematically. I'm more worried balance wise, that no foreign trade can be pretty nasty, but if its only bad effect on three different civics, that might be a concern(on the other hand, if their good things aren't good enough to balance it out on their own, then no one will run the civic without the others, so its a tough balancing act). Perhaps they need some other minor drawbacks besides the foreign trade one. Eg, id like to see guilds get another minor bonus, and a minor malus. No clue what though.
Arete: what about mines giving a bonus point(or 2 for the financial boost) of commerce with arete? This would fit in with the whole money theme of the religion, and make dwarves able to keep up research wise in their hill heavy starts if they can get to arete. If you do this, id tone down the workshop boost, to be only commerce, or perhaps 1 hammer and the commerce. I kinda like the idea of turning all of the +hammer buildings into having weakish commerce boosts to go with them though.
For duty: I agree that it has useful effects(that should show up in some form somewhere), its just rather redundant with order. I'm not sure what the boost should be though. What about a minor(5%) everything boost(hammers, money, research, food), and a - WW boost? I could also see an argument for a draft/-ww.
For mageocracy. I agree that it would be a huge pain to code something for all mana types. What about if instead perhaps pick a few of the mana that make sense, but are rarely stacked generally(nature and life for food, force and earth for production), and make this the minor boost of the civic, while having the major boost be somehow research related or something that boosts mages(I know at some point someone was looking at having promotions tied to civics, what about all of your mages/archmages getting a free promotion(not sure if adepts should count) that gives them a exp growth rate boost while you stay in the civic(or perhaps you could tie it to the mage guilds, so that you only get the boost while staying in a town with a guild, might leave to less overhead to worry about). Could drop the node bit altogether even or just somehow give a flat boost of 2food/2hammers/2commerce to all node and nodetypes.
Other ideas for the initial civics:
Despotism could have a somewhat decent(but weaker than the current city states), reduction for both of these.(perhaps around -(15-25)% on each?) Edit: I moved this and lost the context. What I meant to say was a -(15-25%) to number of cities and distance from palace upkeeps.
Tribalism: is something like +(10-25)% to settler production possible?
Prudance: could have give like 1-3 free gpp growth to the palace(thinking of more ideas, rather than things that fit the name here)? Would be nice to help boost you at the start, but still something that you would grow out rather rapidly and want to swap up.
Same thing for decentralization, with a flat cash boost from the palace(4-8 points or so?)Might need a name change.
Basically, a bunch of minor boosts to the palace would help kick start the game a little, plus would help with anyone someone stuck with only a few towns, but once you get up and running, you are going to want overall bonuses.
You are going to eventually have to tweak the civ specific ones, esp like lost lands which is rather strong synergeristically, and I'm sure there are others that have been weakened due to you introducing things with similar boosts.
I love the majority of the civics, and the few issues I'm not sure about will likely be smoothed out with some playtesting/balancing. Very nice work here. 
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1:gold per specialist as well. I wanted to do 
per Non-State Religion
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in Capital
, +2 
