Here is example of simple shortcode that will take ID as argument and echo permalink for it:
function link_from_id($atts) {
if( isset($atts['id']) )
return get_permalink( (int)$atts['id'] );
}
add_shortcode('link', 'link_from_id');
Usage:
[link id=1]
PS by the way non-pretty permalinks will keep working just fine if you enable pretty mode later and, if I remember right, will be redirected to canonical pretty version.