Just for clarification, the term "deep web" means any site that standard search engines can't find. For example, the confidential details of your bank accounts are technically part of the deep web. The dark web, however, refers to content that exists on darknets (overlay networks that require particular software or authorization to access).  Tor is one of the most popular examples of a darknet, while I2P is another. Darknet markets (which exist within darknets) are where many of the illegal activities take place.

Now coming to your question. It is impossible to stop darknet markets because it will require a lot money, time and resources. Moreover, those running the darknet markets are hidden behind similar software that preserves their anonymity. What you think government haven't tried. But the thing is darknet is so mssive that it is not feasible  to eliminate it.

So the question of effect on bitcoin wih the end of darknet doesn't make much sense.