I'm not sure if this is what you are doing, but I'll say it anyway. If you are creating submodule1 as 'code' and submodule2 as 'tests', that's a horrible way to organize it. Tests (specifically, unit tests) should be stored with the code that it is testing. Thus, each submodule has src/main/java and src/test/java.
Now, that said, it is plausible that you have a 'common-lib' module, and then additional modules that depend on that lib (e.g. application tier). It is highly likely that you run a test at the application-tier and it invokes code in the lib module. But you get no code-coverage credit for that. Jacoco coverage of the lib will be solely based on the tests in the lib. The 'app' tests only give you coverage of the app. This has to do with the instrumentation that happens when jacoco runs - it's only going to instrument the things local to the module it is running in.
Yes, there is a jacoco-aggregate report, but this will merge the module reports together - single report of each module. It does NOT give you unified coverage of an app-tier test calling lib methods, etc.
Lastly, sonar. I believe as long as you have jacoco files hanging around, the sonar-scanner will make use of them. I think it operates on the raw jacoco.exec file, but may be able to interpret a jacoco-result.xml or jacoco-aggregate.xml. If it is giving you grief, include your pom.xml