I don't think it's currently possible.
It could definitively be a feature request to allow the use of wildcards in preferences paths, like "~/pd-externals/myLib/*"... But I would say it's not trivial to implement to the code.
A workaround is to write a subpatch where you [declare -path] all your subfolders, and copy this subpatch where needed. It currently also works if you nest your list of [declare]s into an abstraction (which makes it easier to copy in application patches), but I hope it will still be the case in the future.