Have a really close look at your transom! If they've worked their way along the stringers to the back end they could get into the transom if the timber stringers went through to the plywood that forms the transom prior to the interior stringers being glassed.
You don't want the transom to be weakened in any way or it could be disasterous! I used to work in the f/g boat industry and we used to glass the transom in first then lay in the stringers and floor supports. If this is how your boat was done no worries, termites don't go through fibreglass. Might be worth a call to the manufacturer on the Gold Coast to see if that's how they do it.