Its a great thing to put on a mystic spring.
See, i didn't realize that the bonus would apply to ANY structure with a morale boost. Are you sure of this? Does this mean also, that a stock exchange will get the bonus from a 100% influense bonus tile? I usually ignore those.
I use spies early, at a low level you can see the destination of AI ships. I like to place them on AI captials that i find, enemy or not. The best use of spies i think is placeing them on farms a turn before your transport gets there, then the population will drop as if there was no farm. So it'll take much rewer troopps to take the planet and/or leave you with a better populated world once you take it. This also damages AI economies but dropping thier tax paying populations.
I guess spies cost more because they have to get the lastest edition of the text book. I mean colledge gets more expensive all the time and yet the professors are the same and the students dont come out smarter than the class that paid less tuition. But making spies cost more makes the game work, it makes you consider when and where to use them, also in the later game your economy is much greater compared to the eary game. Imagine in the late game if everyone could build a spy every other turn. It would suck. As a side, i have yet to have a real problem with enemy spies.
Yes, ANY building that gives a certain bonus will work with a special tile, provided the bonus is outputted as a base value. A Stock Market will receive the bonus from a Ruins tile. A Counter Espionage Center does receive a bonus from a Mystic Spring tile. This much I've seen in game.
However, a Research Coordination Center, Technological Capital or Omega Research Center will not benefit from Research Bonus tiles since they don't give base value output, and instead are mere magnifiers. Same with all Powerplants and the Manufacturing Capital. The Artificial Slave Center, Restaurant of Eternity and all Trade Goods remain unaffecting by special tiles since they give multiplicative galaxy-wide civilization bonuses and not base output.
However, I don't know whether the Political Capital would be affected or not. It gives a base Morale and Influence bonus only to the planet it's built on, which means it should be affected by Ruins or Mystic Springs, but it's also a Super Project, and a Capital, which, according to the Wiki, means that it shouldn't be affected by bonus tiles. Strange paradox.