One-to-one unidirectional relation implementation in Hibernate sucks. You implement it using
<many-to-one ... unique="true">. This creates two indexes in the table for the same field, one for uniqueness constraint, one for foreign key constraint.
Class inheritance when using table-per-subclass is implemented in similar way, again two indexes per field (ID) in child table, one created as primary key constraint, second as foreign key constraint referencing parent class table.
And finally dropping an index in MySQL InnoDB table is very expensive operation – it creates temporary table and reindexes it with remaining indexes. So if you want to drop 4 indexes it will re-create and re-index table 4 times. This can take many hours on any reasonably large database.