I want to use the binaries bwa and samtools in IBM cloud functions. I've tried to include both in the .zip as explained here but both executables are missing some shared libraries. What would be a general approach to fix those sorts of problems? Do I have to create a docker image for that?
You should build and use your Docker image. That is recommended for more complex dependencies. The .zip could work, but it requires some laser focus in catching all dependencies.