Shortcode display CPT Query only showing 1 post?

As @Milo said in his comment above, you need to use concatenation as this is a loop your in. So you need to add a value each iteration not replace it. Your $output="" needs to become $output .= ''. Notice the point/dot before declaring the value, in PHP this is used for concatenation.

//the loop
        while($gallery_query->have_posts() ) : $gallery_query->the_post();

        $output .= '<article class="masonry-entry" id="post-' . get_the_ID() .'" ' . get_post_class() .' >
                <div class="masonry-thumbnail border">
                    <a href="' . get_post_permalink() . '" title="' . get_the_title() . '" class="inner-shadow">' . get_the_post_thumbnail(get_the_ID(), 'masonry-thumb') .'</a>
                </div><!--.masonry-thumbnail-->

            <div class="masonry-details">
                <h5><a href="' . get_post_permalink() . '" title="' . get_the_title() . '"><span class="masonry-post-title"> ' . get_the_title() .'</span></a></h5>
                <div class="masonry-post-excerpt">
                    ' . getPostLikeLink(get_the_ID()) .'  <p class="post-comment"><a href="' .get_post_permalink() . '"><i class="fa fa-comments qcomment" title="Comments"></i></a> ' . comments_number( ' ', '<sup>1</sup>', '<sup>%</sup>' ) . '</p>' . getBookmarkLink(get_the_ID()) . '
                </div><!--.masonry-post-excerpt-->
            </div><!--/.masonry-entry-details -->  
        </article><!--/.masonry-entry-->';

        endwhile;

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