Just a regular user here. Also I have no experience compiling for ARM. On my system, vkd3d.h was installed in /usr/include/vkd3d. You can get to the source by starting at the winehq write up on it:
I guess it's either not installed or the wine configure script is not finding it for some reason. First determine if it is installed, a very brute force way to do that is to enter the following command as root or as a sudo command: