In response to the general question "is splitting databases a legitimate security measure", isolation is indeed a well-known, useful tool for implementing security. Whether its benefits outweigh its drawbacks (generally, additional complexity) is very much situation-specific and I don't know the answer in your system's case.
Suppose for example that someone wanted to build an analytics application on top of your data. It would be very useful to have the mapping data completely out of the picture. If the analytics app is breached, the mapping information is not at risk.
Responding to some comments below, even in your system's specific case, it's not a foregone conclusion that "breaching the system" amounts to breaching all databases at once. Suppose that an attacker exploits a SQL injection vulnerability in your application. If the mapping data is separate and hardened (extra controls on code that accesses mappings, say), then isolation can be the difference between exposing unassociated data and associated data.
Not arguing that it is a good design for your system. Just trying to explain different kinds of rationale that can go into this.
I'm using the same isolation strategy in a similar situation. The "databases" in my case are configuration repositories. All of the preprod configuration goes in one repo and the production config goes in a separate repo. All developers have access to the preprod repo, but only release engineers have access to the prod repo. The rationale is that I want defense in depth: while I could certainly implement access controls on the individual repo folders, I'd rather make the production config simply network-unreachable to all unauthorized staff.