The issue is bigger than WPTouch, and the answer is to stop defining shortcodes inside of a specific theme. Instead of defining shortcodes in the functions.php file within a particular theme (or adding an include in that file that points to a short codes.php), just create a simple plug-in for your shortcodes. That way, your shortcodes will continue to work when you switch themes, and they will continue to work when you view the same site on a desktop, with your regular theme, and on mobile, with WPTouch.
Another nice benefit of using a plug-in for your shortcodes is that you can use the built in editor screen to make changes to your shortcodes. The reason why that is good is because if you make a mistake in your code you will be prompted with an error message before the edit is saved. That will prevent your temporary errors from temporarily breaking your site for your users until you fix the error.
If you have never created a plug in, it is really easy. Its just a php file that you save in your plug-in directory. For an easy model, if you have never done this, just take a really simple plug-in, such as Hello Dolly, and copy the file, change the name of the file and the information at the top of the file, and delete the code.
If you are nervous about just cutting and pasting all of your shortcodes from your functions.php to your plug-in, you can take it step by step to isolate and troubleshoot each step: Start with your plug-in that contains no code and activate it through the administrative menu for plugins. If that worked fine, then go to your functions.php file, copy one (or all) of your shortcodes and paste them to a text file temporarily and either delete them from your functions.php file, or comment them out and save. Now check to confirm that your shortcodes are not working on your site. Next, paste those codes into your plug-in and confirm that your shortcodes are working. Thats it.