Sorry for the late reply.
Again, do you have any actual evidence that SHA-256 repositories in version 3.0 won't be able to reference SHA-1 repositories as submodules?
Based on the design doc it looks like git will include both hashes during the transition, specifically to allow two-way communication with SHA-1 remotes. You may not be able to include a random stranger's SHA-1 submodule via a shallow clone, but just doing a full clone sure as heck looks like a supported usage.