QUOTE(Lopov @ Nov 17 2014, 04:17 PM)

... If I click on them, nothing happens....
Do you get the [E] and the appropriate "use shrine" message, but they don't activate, or are they acting like a regular static that you can't interact with, like a rock?
If a mod has replaced the shrines with statics, by the usual process of overriding the reference, then removing the mod should revert them. If they were deleted by script and a new item placed, they might now be persistent in the save game. Open the console and click the shrine. If it's replaced, then the refid won't begin with '00' any more.
If the refids are still 00, it's possible that there's still a mod script in the scripts folder that's doing it. When you uncheck the esp, the pex files remain, and can still screw up the game. Look in the folder for anything with shrine in the name as a possible culprit.