For a project of this scale, I'd recommend a pilot system first. Without any real measurements to start with, it's hard to know what to sweat about.
Spring itself is very small. The "gotcha" is that Spring applications -- and that definitely includes Spring Boot apps -- often employ one or more of Spring's add-on modules. As a rule, those modules are also compact and efficient, but what's efficient for most cases isn't necessarily efficient for you, and again, that requires measurement.
Spring Boot apps each contain their own private webapp server, e.g., Tomcat. Tomcat isn't very greedy, but if you have a lot of them, it can add up. A primary benefit of Spring Boot is that you can spin up/down multiple instances in a distributed elastic environment, but if that isn't a good fit for your actual workload, it might be more profitable to install multiple microservices in a Tomcat instance(s) or even look at commercial servers like WebSphere and WebLogic.
Before writing a lot of ETL services, consider the dedicated ETL products such as Hitachi's Pentaho, Available bot in free community editions and with commercial support. They are extremely efficient and can typically be "programmed" by non-programmers.
I definitely recommend JPA over brute-force JDBC. It scales much better both in performance and in maintainability.