To keep the database small, you can remove all "irrelevant" tokens from it by clicking File->Prune. Irrelevant tokens are those that do not contribute to the probabilities generated by JunkBroom.
Note, however, that this must not be done with very small databases. The implications are quite intricate, and pruning may impact accuracy quite a bit.
There is no need to do this unless your database is very large and you are quite sure that classification is very good (it won't get worse with the current database, new additions will just be classified less accurately).