Modules in ISPConfig are self contianed, this means that they shall have their own templates folder for their web forms. These templates are not part of the theme as they should exist only once for all themes and dont contain theming information or styles, otherwise it would be nescessary to edit every theme when we add a new field to a web form.
Just an example:
If you maintain a theme for ispconfig were then you would have to change your theme for every new feature that we add in ispconfig or your theme will stop to work corrcetly. And you will have to maintain different versions of your theme for ecah ispconfig version, I dont think that this is what most users want.
Nevertheless we can add themes/*theme-name*/ to the paths were the template engine searches for files, but I'm not sure if this is a good idea as many users will start complaining here in the forum if they updated their ispconfig and it stops working then due to the fact that the theme does not support new features.