I would suggest to have a look at LMDB (which is the most efficient engine for OpenLDAP, and used in a number of other open-source projects).
LMDB is an embedded key/value store, with a Berkeley-DB or LevelDB like API, does not have to store everything in memory, and can support access from multiple processes. There are Node.js bindings:
- https://github.com/Venemo/node-lmdb
- https://github.com/rvagg/lmdb (see also this post)