Difference beetween mysql 5.5 and 5.6
EXPLAIN the SELECT subquery.  (This will workaround the point that jynus brought up.)

Your KEY vigi_unique can be made somewhat better by adding id onto the end of it.  This will change the EXPLAIN to say "Using index" because it will be a "covering index".

But the real reason for 5.6 to be faster is ...


The subquery is after "LEFT JOIN", so 5.5 evaluates it over and over (I think), and
5.6 will create an INDEX (on the fly) for the subquery.


Suggest using EXPLAIN FORMAT=JSON SELECT ... on 5.6 to see a little more.

You should consider moving to InnoDB.

Another way to "dedup" is to create a new table (with a UNIQUE index to prevent future dups), populate it with INSERT ... SELECT DISTINCT ..., then RENAME TABLE to move it into place.