Is there a triple store to manage OWL as named graph and compatible with OWL-api?-Collection of common programming errors

Having multiple ontologies and storing them in different named graphs is not a problem at all and can be done in any triple store. However, if ontologies are interconnected, and you want to take advantage of the interconnection, then you won’t probably have direct support for your case with an out of the box solution. But it depends on what you mean by “interconnected”. Does it mean the ontologies import others? Does it mean you have ontology alignments connecting the ontologies? Do you have other types of links between ontologies? Transformation rules from ontology instances to other ontology instances? Etc.

As for your second question, I’d say you can probably do that with a number of tools, but you would have to add your own custom code to make it all work together as you’d like.