Jetpack's Mobile theme is a completely different theme, that is loaded when your readers access your site with a mobile phone. As a result, all functions that were included in your desktop theme won't be loaded in the mobile theme.
If you wanted to use custom shortcodes in the Mobile Theme, these shortcodes would have to be added via a plugin, that would be loaded on any theme you would use on your site.
I would consequently recommend that you move the shortcodes from your existing theme into a separate plugin. This will also be useful whenever you decide to switch themes; anything that customizes your site content is better loaded in a plugin; anything that customizes your site layout/design can be in a theme.
I hope this helps.