When you right-click to create your Simulink behavior from System Composer, make sure you choose "Subsystem Reference". Simscape models do not support physical ports crossing the model reference boundaries but they can cross subsystem reference boundaries.
Simulink has two kinds of files - Model Reference and Subsystem Reference. These are treated slightly differently during simulation and code gen. The models are atomic units whereas the subsystems are meant to be pieces of a larger model. Root-level Simscape ports will only work in a referenced subsystem.
The HydraulicPump_Model you shared is a model reference with physical ports at the root level, this is not supported by the Simscape library. The good news is that you can convert the subsystem in that model to a subsystem reference and link your System Composer component directly to it.
Here are some screenshots I made using the model you shared:
1. Right-click your existing subsystem and convert it to a Referenced Subsystem:
2. Give it a name
3. In your architecture model, right click a component and choose Link to Model... then link it to your new subsystem reference.
4. All done!
