Theme specific Drupal modules? Possible?
Themes are enabled/disabled in Drupal by altering the flag in the database table system. And these settings are common for all the users irrespective of which device/ how they are accessing your page. 

So in your case it is about making sure that only the files from necessary modules are loaded based on the current theme.

You can use $theme global variable to find out the current theme, and then based on that you can fetch the files from the necessary modules only. You can check the code from js module how the second part can be implemented. You need to have patience though ;)