When having a @OneToMany annotation on an entity and later changing that to @ManyToMany, Hibernate does not drop the unique constraint. It simply leaves the constraint intact.
Dropping and letting Hibernate regenerate the table does not add the unique constraint (works as expected). This means you'll not be able to insert multiple entries in the table, unless you regenerate it.
Created Table thus far:
Likewise, changing @ManyToMany to @OneToMany will add a unique constraint. Inserting multiple values will however work fine.
Re-generating the table will add the constraint just fine.
SQL thus far:
Attached are the pretty basic entities I've used to confirm this behaviour.
Hibernate 4.1.1, bundled with JBoss AS 7.1.1
Microsoft SQL Server 2008