podrias usar UNION ALL, solo colocalo entre los querys, saludos
Código:
SELECT COUNT(p.pub_id) AS pub, p.pro_id FROM publicacion p
INNER JOIN categoria c ON c.cat_id = p.cat_id
INNER JOIN proyecto pr ON pr.pro_id = p.pro_id
WHERE c.cat_pa = 17 AND p.doc_id = 1
GROUP BY p.pro_id
UNION ALL
SELECT COUNT(p.pub_id) AS pub, p.pro_id FROM publicacion p
INNER JOIN categoria c ON c.cat_id = p.cat_id
INNER JOIN proyecto pr ON pr.pro_id = p.pro_id
WHERE c.cat_pa = 25 AND p.doc_id = 1
GROUP BY p.pro_id
UNION ALL
SELECT COUNT(t.tes_id) AS tes, t.pro_id FROM tesis t
INNER JOIN categoria c ON c.cat_id = t.cat_id
INNER JOIN proyecto pr ON pr.pro_id = t.pro_id
WHERE t.doc_id = 1
GROUP BY t.pro_id