Hightlight search-terms with functions does remove or disable other filters?

Usually, for filters like these content is passed into the filters, processed and passed back out. That is more or less the definition of a filter. Of course that isn’t strictly true. You don’t have to take input and you can wipe out “input” content if you want, though it is probably not a good idea most of the time.

function search_excerpt_highlight($excerpt) {
    $keys = implode('|', explode(' ', get_search_query()));
    $excerpt = preg_replace('/(' . $keys .')/iu', '<span class="search-highlight">\0</span>', $excerpt);
    echo '<p>' . $excerpt . '</p>';
}

The way those functions are written they would wipe out any filter processing that executed earlier in the queue. That is, filters are added to a kind of execution stack and then applied one by one. Anything earlier before those filters would be lost since they aren’t accepting information, the are just grabbing the raw data with $excerpt = get_the_excerpt(); and $title = get_the_title();