There were several patches in Drupal 6 which removed duplicate indexes (and/or added missing ones), so it's likely that pretty much all of these issues are resolved.
Nat
Performance and the size of the index file. My reference is for Drupal 5 and I do not know what may have changed for Drupal 6 yet but there are a number of duplicated indexes on some of the tables. A column might be used as the first position in combination with another column to create an index and also be declared an index alone. This becomes a duplicate index and isn't needed. Some tables do not have unique or primary key identifiers a big performance hit.