The airport grounds and the Airport Express right-of-way have not been sealed off. The sort of folks who are doing the sort of things being done in Mongkok are perfectly capable of figuring out how to bring trouble back to Lantau if they ever decide to go that route again. Let's not talk details. We should accept that risk remains, including risk of cancelled flights for transit passengers, so long as there's trouble in Hong Kong.
You are correct that it is possible for a major airport disruptions to happen but do you think it is probable?