Easy-peasy explanation:
Game stores settings in application data folder, not in main one. If you deleted it manually( 0AD developers made PROPER uninstaller, right? >_< So annoying in other games) mod was left enabled in the settings. Because of some reasons, if game can't find folder of enabled mod, it creates it itself. That's it.
Proper installation: somedisk:\0 A.D. alpha\binaries\data\mods\Hyrule
Hyrule is folder with technical folders and uninstall.exe.
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