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Disclaimer: I haven't used ROS2.

import some_special_package within my ros node. I rosdep installed, (skip) ran ros2 run my_pkg my_node, and I get a ModuleNotFoundError.

The one prints that error is Python, which is looking for a Python module. The name of a Python module can be different from the Python package that includes the module of your interest.

Assuming rosdep install part passed without errors, the PyPi package you wanted is likely installed (but make sure if that's the case. Depending on the option, rosdep ignores the error).