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No, A and B will not be given the same value_id in the RDF_VALUE$ table. They are after all different nodes, which are connected by the sameAs relationship.
All nodes related through the sameAs relationship can be retrieved through SDO_RDF_MATCH queries:
SELECT A, B
'(?A http://www.w3.org/2002/07/owl#sameAs B)',
You might want to do inferencing (entailment) using the owl:sameAs property - for example you might like to infer:
A owl:sameAs B, B myProp C
=> A myProp C
Such inferencing support (for OWL properties like sameAs) is supported in the recently releasd 11g. It is not supported in 10gR2 (which only supports RDFS and user-defined rules).