Simple ontology definition and query problem

Web Ontology Language is designed to describe the large world, not little ones. That is why it uses the Open Wold Assumption. Just ask yourself, what if someone on the Internet states that Hippopotamus1 isin Box1? There are some techniques however to "close the world" (for example, using oneOf). Pellet ICV also supports closed world assumption. But it is not the standard behaviour. See also this question.

Regarding your example: you don't have to define each box as "Box and (include only (Ball))". Defining the Box class as Object that include only Ball should be enough. But this will not prevent anyone to state that Hippopotamus1 isin Box1. This statement would just mean that (surprisingly!) Hippopotamus1 is not only a Hippopotamus but also a Ball.

Assuming your query engine is supporting an entailment regime that is expressive enough to give you the intended conclusions, you may want to use a SPARQL query like this one:

SELECT ?object ?class WHERE {
    { 
      :box1  :include  ?object .
      OPTIONAL { ?object  a  ?class .}
    }
   UNION
    { :box1  :include  [ a ?class ] }
}

which would give you a binding of variable ?class to :Ball with ?object unbound, plus any other object that may have been declared as being in the box.