A SP can use whatever data model it desires (TAS3 Architecture is not prescriptive in this regard) in storing the data about the Users as long as it meets security and privacy guarantees detailed in Annex C "Compliance". The persistent pseudonym of the User suggests an obvious database key, but other arrangements are possible.
TAS3 Architecture foresees aggregation of data from multiple sources with its support for policy aggregation. One common realization of this approach is to consider a document as a collection of external data streams, please see [TAS3D81RepoSW]. This approach will be supported by some of the TAS3 software deliverables (e.g. output of WP8).