suggestions on building Research portal for multiple studies and sites

We currently have a Drupal 7 portal collecting research data for multiple studies (set as individual content types), for multiple sub-projects (individual content type set as entity references), across multiple clinical sites (set as taxonomy).
Please refer the pic attached for the current structure.

We have used node access, field permissions and taxonomy access control contrib modules for configuring permissions.

With rapidly increasing number of projects and clinical sites, we have ended up having a lot of content types in a single database, and the portal performance is getting less efficient.

We are planning to migrate to Drupal 8 very soon and wanted some suggestions on whether to use multisite options or domains, use single database or multiple database?

We also have a custom LIMS module for our laboratory management, that is used across the studies and sites. Meaning, we have few serial/integer fields that is unique across the studies and want to retain this uniqueness. Any suggestions on keeping the uniqueness of these fields/IDs if we want to go multisite-multi-db way?

In the later stage, we also want to add an Intranet website to be accessed within the organization.