You could indeed use union, why not? But why use UNION ALL, and not just UNION? Just pick the one common column:
SELECT 1
FROM
(select A.fk from A inner join C on A.FK = C.pk
UNION
select B.fk from B inner join C on B.FK = C.pk) AS bothTables
WHERE fk = 'desiredValue';
This would work just nicely.
Tested it on the following tables in MySQL, with myValue = 1, just to verify.
mysql> select * from A;
+------+--------+------+
| pk | value | fk |
+------+--------+------+
| 1 | ape | 2 |
| 2 | fjfjfj | 3 |
+------+--------+------+
2 rows in set (0.00 sec)
mysql> select * from B;
+------+--------+------+
| pk | value | fk |
+------+--------+------+
| 1 | katt | 1 |
| 2 | fjfjfj | 3 |
+------+--------+------+
2 rows in set (0.00 sec)
mysql> select * from C;
+------+-------+
| pk | value |
+------+-------+
| 1 | hei |
| 2 | nei |
| 3 | jeg |
+------+-------+
3 rows in set (0.00 sec)