I just stumbled upon these two different dir names when upgrading to opencv3 and assumed this was controlled by debian packaging and has been an oversight in the transition. The digikam compiling issue was resolved on the spot back then. This report can be closed - thanks for your explanation and sorry for wasting your time.
- Bug#880438: libopencv-core-dev: installs headers in opencv2... Simon Frei
- Bug#880438: libopencv-core-dev: installs headers in op... Mattia Rizzolo