In a native query "?" means insert the parameter bound for the current index, i.e. the first ? is the first parameter, the second ? is the second parameter.
"?1" means insert the query parameter bound to 1. The only time you would use this is if you wanted to insert the same parameter twice, or wanted control over the JPA Query parameter order.
em.createNativeQuery("select salary, ?1 from emp where salary > ?1").setParameter(1, 100000).getResultList()