You can use the count
property of the taxonomy term and if it is > 1
, then show the term linked to archive.
// inside loop, get the terms of a custom taxonomy for the current post
$terms = get_the_terms( get_the_ID(), 'your_custom_taxonomy' );
// cycle the terms and display the name, linked to archive if term count is > 1
foreach ( $terms as $term ) {
$link = $term->count > 1 ? get_term_link( $term, $term->taxonomy ) : FALSE;
echo '<li>';
if ( $link ) echo '<a href="' . $link . '">'; // open link if needed
echo $term->name; // always show term name
if ( $link ) echo '</a>'; // close link if needed
echo '</li>';
}