Can someone tell me if an Indie licence (which does not allow you to integrate with commercial licence projects -- i.e. file format can not be opened) is still commonly used by freelancers when working with studios?

That is, do studios generally require you share Houdini project files that are compatible with their commercial licence, or do you just send them a rendered output?

Indie licenses are not compatible in commercial environments. What you can supply to a commercial vendors using your Indie license is rendered frames and animated geometry. You can rent commercial licenses if your vendor is intent on obtaining the HIP file.
Another option is to just kick out animated VDB sequences and or Alembics and produce a companion render file using Blender, which you can deliver to a studio.