So, is my assumption correct: if no --add-modules and --limit-modules are specified, the set of observable system modules consists of all system modules except java.se.ee?
In short, yes that is correct. 
The default set of modules enabled in Java 9 are known as the root modules. 
Per JEP 261, the default set of root modules are defined as:
- The java.se module is a root, if it exists. If it does not exist then every java.* module on the upgrade module path or among the system modules that exports at least one package, without qualification, is a root. 
- Every non-java.* module on the upgrade module path or among the system modules that exports at least one package, without qualification, is also a root. 
Here is a nice graphic of what is included in the java.se module:
 (Source: Java 9 javadoc)
(Source: Java 9 javadoc)
Like the java.se aggregate module, the java.se.ee module itself does not provide any classes, it is an aggregate module that includes the following modules:
java.se
java.activation
java.annotations.common
java.corba
java.transaction
java.xml.bind
java.xml.ws
Is there a reliable way to know the exact list of default observable system modules? I know there is a --list-modules option, but it lists all modules including java.se.ee.
Your terminology is slightly off here. In Java 9 a module is observable if both of the following are true:
- the module is a system module (i.e. comes from the JDK) OR it is added to the module path
- the module is not excluded via --limit-modules
This means java.se.ee is observable by default.  
I think instead you are wondering what modules are the default set of root modules? In which case, see the above definition of root modules.