I found this as to why it might be:
"As the mesa arm side GL driver is going to become the standard in the future, we’d like to avoid confusion when linking with either the arm side driver (/usr/lib/arm-linux-gnueabihf) or the gpu driver (/opt/vc/lib).
As such applications built to use the gpu driver should now link with libbrcmEGL.so/libbrcmGLESv2.so rather than the ambiguous libEGL.so/libGLESv2.so libs." - https://www.raspberrypi.org/blog/raspbian-stretch/
Also, finally got it building (running rpi-update on Stretch pulled in old name GLES libs which fixed GL build/linking errors) and input working - it turns out all I needed was to add libibus-1.0-dev (labelled as optional in build instructions but I found it not to be optional for RPi with versions of urho3d 1.6+)
While most samples worked fine, 19_VehicleDemo caused a flashing screen (and nothing else) and the ragdoll sample had strangely all the left legs of the dummies stretching out to a point in the sky.