This is very bad news.  What you are in effect saying is that it is just fine with the database for 60% of the tables to silently accept duplicate rows.  Even if the application running against the data today enforces no duplicates, or even if the business logic today says duplicates are fine you are violating one of the key rules for the relational model.  This is significant because the relational model is based on the mathematics that guarantees that  applying relational operators to relational tables produces relational result sets.

Further, duplicate data will produce all the well known problems sooner or later.

Finally, even if you have no duplicated data today because of the applications sooner or later someone will access the data with another application or tool and then you will have duplicated rows.

I would suggest that you figure out what this means in application or business terms, inform your management, and if the problem is not fixed that you provide yourself with CYA documentation.

Allan