@Seán O'Halloran I am pretty sure I figured out a workaround that you can try, which avoids the symlink issue. What I will say though, is that this query is not kind to your endpoints. From a resource perspective, any query that hashes hundreds or thousands of files on the filesystem is going to cause a significant performance impact and should be considered (or more likely avoided) carefully:

WITH mounted_volumes AS (
    SELECT path 
    FROM mounts 
    WHERE path LIKE '/Volumes/%'
    AND SPLIT(path, '/', 1) NOT IN ('BOOTCAMP'))
SELECT hash.path,
       hash.md5,
       file.size,
       file.block_size,
       file.type,
       file.uid,
       file.inode
FROM file
    LEFT JOIN hash USING (path) 
WHERE file.path IN (
   SELECT file.path 
   FROM file, mounted_volumes 
   WHERE file.path LIKE mounted_volumes.path || '/%%' AND file.size > 0);