Not all the object databases are equal, some are faster and some are much slower.
Since you mentioned JPAB, you should also check other pages, e.g. http://www.jpab.org/Hibernate/MySQL/server/ObjectDB/ObjectDB/embedded.html
But also consider that the page that you mentioned shows that the combination of DataNucleus with db4o is extremely slow. It says nothing about db4o without DataNucleus or DataNucleus without db4o, which may be better. Anyway, there are other object databases, including Versant Object Database and our own ObjectDB, which are much faster.
Try to create a test application in which MySQL/Hibernate is faster than Versant Object Database, ObjectStore or ObjectDB, and you will see that it is much more difficult.