We are using the C version of BDB (which is also GPL) because this makes potentially accessible from C++ if anyone cares to port the Java code :) The Java version actually started started as prototype that would become the "real" C++ version.

As for the license, HyperGraphDB is LGPL in the sense that a version where the BDB dependency is removed will have no strings attached for commercial use. Architecturally, HyperGraphDB has a low-level storage layer that is isolated by a handful of classes and is currently implemented with BDB. So it is not such a major undertaking to replace it, given a suitable (in terms of license, functionality etc.) replacement.