consulta mysql muestra varias tablas de una columna de ID

Tienes que unirte dos veces. Dale a la tabla diferentes alias para que puedas distinguirlos.

SELECT h1.name as host_name, h2.name AS template_name
FROM hosts_template AS t
JOIN hosts AS h1 ON t.hostid = h1.hostid
JOIN hosts AS h2 ON t.hosttemplateid = h2.hostid