Is it always better to just use query.setParameter() instead of type-specific methods like query.setLong(), etc., since Hibernate would automatically do the correct type-matching based on the mapping file? Is there any cons to this?

One advantage with using setLong() and other type-specific methods are that you get compile-time errors in case you change parameter type. With setParameter() you'll only get a run-time error which may be harder to track down.

Thank you!