Hi nicheru,
How did you create the metaboxes, by hand, or are you using another plugin to create them? If by a plugin you might be out of luck unless the plugin includes an option to allow shortcodes.
If you actually coded them yourself, you should be able to manipulate how the data is “printed” to the frontend of your site. All of the data that is saved in the metabox will be stored as metadata attached to the post/page the metabox is on. You must have created a function that take this metadata and does something with it on the frontend such as echoing it out. So for instance, if you are echoing it, something like this might work: echo do_shortcode( $metabox_content ).
I hope this helps a little.
Nick