The long term consequences for Hong Kong are these:
1. Beijing will go all out to marginalize Hong Kong.
Mainland China has been trying its hardest to keep Hong Kong in the lead as a financial center, sea transportation center. They've been holding off developing similar sectors in other major cities such as Shanghai, ShenZhen and GuangZhou. Incident like this makes them realize that Hong Kong can be played by foreign hands. It is important to diversify and reduce its weight on China's economy.
2. Beijing will gradually increase tax for products from Hong Kong.
Currently mainland gives enormous tax benefit to Hong Kong products, almost 0%. They also don't collect any tax at all for administration. It is unheard of that any country would not collect any local tax from a region that accounts for 3% of its GDP. The HK'ers have been spoiled so much that they think they are entitled for everything. It is time to take that away and make them earn everything.
3. The cost of water, gas and other resources from mainland to Hong Kong will go up closer to their true market values.
Hong Kong relies 100% on mainland for water. And they've been getting it cheap year after year. They must pay at least close to the resources' market price. Why would mainland subsidize the "superior residence" of Hong Kong?
4. Beijing still gets to appoint Hong Kong's governor
You didn't ask for your own governor for the past 100 years under the U.K. rule, you don't get to ask that now either.