The way to go on very large amount of data without create too large file is to use multiples containers. You should cut your data model into multiples containers (aka files).
Each file will contains some part of your model. Then by querying the good container, you should be able to retrieve yours objects; The joins (if need) must be done by hands.
If you have so few class in your model that it don't make sense to cut it, then I'm not sure db4o is way you need. Maybe a simple file with very tiny serializations should best fit yours needs.