That shouldn’t be particularly problematic, it’s just some (unused) submodule folders that get left over from the branch switch, since master has some new submodules that aren’t in the Sub-4.0 branch (which the ArduSub-stable tag is currently sourced from). It’s best to avoid adding them to the tracked history and committing them, but even if you do accidentally do that they still wouldn’t have any code that actually tries to use them.
Ahh yes, that’s an issue that came up recently, and it’s an actual error, so it could stop things from working properly (in particular, because the submodules don’t get updated to track the branch, they would still be on the newer versions from master, which may have functionality differences). We unfortunately haven’t yet had the time to fix it properly, but that comment covers a workaround that can be used in the meantime.