No, I don't think subtrees can really help you with this unfortunately. At least not directly. Using the flattened mode might help, but then you'd be back to your problem with signing them. The subtree merge commit does record the original SHA, so I suppose you could verify as a separate step if you needed to that that merge commit is indeed the result of a correctly signed SHA somehow.

But I think for your use case you're probably stuck with submodules.