I have faced the same issue when use EntityManager.createNamedQuery
(guess the same issue with createNativeQuery).
In case you are going to pass nullable
parameter to Query then use TypedParameterValue which allows to pass the type.
For instance:
setParameter("paramName", new TypedParameterValue(StandardBasicTypes.LONG, paramValue));
Here you explicitly set the type of passed value and when you pass null value as processor know the exact type.