Test case: (from Rien) ...
Ebean.find(Order.class) .where().eq("customer", null) .findList();
The issue here is actually with the NullExpression object.
For the case of assoc one properties like "customer" ... the expression objects like isNull() eq(), in() etc ... need to translate "customer" into "customer.id" and use the id of the bean.
The isNull() expression is not doing this.
See TestQueryNullAssocOne.
Fixed in HEAD.