Some of our builds started breaking over the weekend, because catkin-pkg-modules has disappeared from the pypi index. Was this an intentional change?
Yes, that package should have never been published to PyPI. You should use catkin_pkg instead. Both packages in PyPI were identical.
The separation in two packages catkin-pkg and catkin-pkg-modules is only for Debian packages to enable installing python-catkin-pkg-modules and python3-catkin-pkg-modules side-by-side.