I asked on the box developer forum, and it turns out there is an API which will do what I need called the preflight check.
Its purpose is to see if files exist before you upload them which is why I hadn't twigged it is useful, but it does exactly what I need to avoid listing the directory as in it turns a (fileName, directoryID) into a fileID. I needed to call another api method to turn the fileID into the full file info, but I think both these API calls will be very quick compared to listing directories.
I haven't attempted to performance test these though as exactly how they perform will depend on your workload, but I'd be grateful if you'd try to do that @durval to see how much (if any!) performance gain you get when syncing large directories.
v1.64.0-beta.7344.0299ce2a7.fix-box-metadata-for-path on branch fix-box-metadata-for-path (uploaded in 15-30 mins)