How to deal with inter-dependencies with jucer projects?

In that case you can treat your library like any other external library. You can add this in the projucer and the exporter will add the linker call to the project file.
There are already very good examples how to achieve this, so I simply quote an arbitrary answer with nice screenshots:

That approach worked for me using the sodium crypto library…

Or you can use the forum search for “external library” for alternative solutions…

N.B. I also found the solution @adamsky proposed very helpful. The big benefit is, that you can browse the source code and debug much more easily. But as you said, you probably have good reasons to have it as library too.