It doesn't look like there's a simple way to solve the problem using just built-in functions.
This (at least logically) should work.
$search_terms = array('a', 'b', 'c', 'c', 'd', 'd');
$search_types = array( 1, 2, 3, 4, 5, 5);
$terms = array_fill_keys($search_terms, array());
// Loop through them once and make an array of types for each term
foreach ($search_terms as $i => $term)
$terms[$term][] = $search_types[$i];
// Now we have $terms = array('a' => array(1),
// 'b' => array(2),
// 'c' => array(3, 4),
// 'd' => array(5, 5)
// );
// Now run through the array again and get rid of duplicates.
foreach ($terms as $i => $types)
$terms[$i] = array_unique($types);
Edit: Here's a shorter and presumably more efficient one where you end up with a less pretty array:
$search_terms = array('a', 'b', 'c', 'c', 'd', 'd');
$search_types = array( 1, 2, 3, 4, 5, 5);
$terms = array_fill_keys($search_terms, array());
// Loop through them once and make an array of types for each term
foreach ($search_terms as $i => $term)
$terms[$term][$search_types[$i]] = 1;
// Now we have $terms = array('a' => array(1 => 1),
// 'b' => array(2 => 1),
// 'c' => array(3 => 1, 4 => 1),
// 'd' => array(5 => 1)
// );