The strings is readed at runtime and as fast they are changed in the resx-file they are updated. They are not stored in database.
The folder structure that the files are using reflected the “old” modules and we have one file for each module. When we started with the new BO UI we decided to only have one file and that is loaded from Administration folder. Example on folder names for the CMS/ECommerce is for ModuleCMS and ModuleECommerce.
The accelerator templates in Litium 7 have all their strings in the administrations-folder, even that the entity is for different types.