Many thanks to all for updated info, and the very valid points from @ Steve M.
As an update - we have managed to find a very helpful person at the Shekou ferry who stated:
'As a general rule, when the severe disruption was happening, they could not keep up with the cancellations and changes by the minute, so they only allowed passengers with confirmed tickets on 'non' asian carriers to board. This was on assumption that the longer distance flights would have an incoming plane already en-route / had arrived at HKIA. However , as usual with China, there were a few exceptions, especially early evening, when the picture became clearer on departing evening flights, although they had to deny people check in for the last 2 ferries in the evening as they were full with most additional travellers having made the journey from HK via Shenzhen".
So, I was not the only person who thought it a good idea.
Reading into it, keep your eyes on events on the day you are flying out, this is a possible route, however, it will still have it's own risks.