Hello,
We are migrating from Kodo (JDO) to Hibernate and when creating DDL scripts from JPA and Hibernate annotations, Hibernate SchemaExport adds NOT NULL constraints on columns in join tables.
However, we are using a legacy schema where join tables allow null columns in join tables and it is actually used - we have a lot of records where one field is null.
So far we have been using Kodo and it had no problems with it. Kodo did not create that NOT NULL constraints.
I found in Hibernate sources that it is hardcoded in method with a comment
Is it possible to stop Hibernate from creating NOT NULL constraints? If so, could it cause other problems when reading or saving data from/to such a join table where some fields are null?
We are using Hibernate 4.2.18.

The value is indeed hardcoded and you can't override it with the @JoinColumn annotation.

However, why do you use the auto-generated schema? That's only useful for prototyping and may be for generating the first schema skeleton that you validate prior to using it as the first schema migration script.

You should be using an automatic schema migration tool such as Flyway instead.