I am trying to hide a custom post type category to logged in users with Pre_Get_Posts

OK, so you have few mistakes in there.

1. field can be term_id or slug, but not id.
2. tax_query should be array of arrays and not an array.

So here is fixed code:

function exclude_category( $query ) {
    if ( is_user_logged_in() && $query->is_main_query() ) {
        $taxquery = array(
            array(
                'taxonomy' => 'project-type',
                'field' => 'term_id',
                'terms' => array( 94 ),
                'operator' => 'NOT IN'
            ),
        );

        $query->set( 'tax_query', $taxquery);
    }
}
add_action( 'pre_get_posts', 'exclude_category' );

It’s not tested, but I’m pretty sure it should work just fine.