When hibernate creates sql statement for reading from sequnces it doesn't us the hibernate.default_schema property. Is there some setting to force this?
If I specify the schema name in mapping, it is added to the read sequence sql statement, but what I would like to awoid hardcoded schema name in mapping file.

Unfortunatly no. This is a bug by design in Hibernate and is too hard to solve.
What you can do is to use ant and replace a token not to hardcode the schema.