I have run percona script pt-duplicate-key-checker on moodle 2.7 database and many tables have redundant indexes.
For example table mdl_user_enrolments have the keys
`mdl_userenro_enr_ix` (`enrolid`) and
The key mdl_userenro_enr_ix is redundant because it is the left-prefix of index `mdl_userenro_enruse_uix.
Duplicate indexes like this can hurt performance, but sometimes the redundant index makes sense when the full index is a lot longer.
The redundant keys need to be reviewed to see if some of them can be deleted to improve moodle performance.