What you are saying makes common sense, but the law and common sense has little to do with each other. From your drug dealer example before, its not illegal to sell a bong but it is illegal to sell pot. Proving what something is intended to be used for assumes you no what the person making it is thinking. The person selling the bong can say it is to be used to smoke tobacco. The maker of the program can say it should be used to share none copy written material. Unless they have proof that the maker advertised its use or have some other type of proof that this was his intent, it sets a bad precedent.
But you left out a major part of my example. Getting paid by a drug dealer to sell drugs at your shop. Correct by itself there is nothing wrong with the bong or crack pipe, but once you put a person at your shop selling drugs and giving you some of the profit things change.
Just positing "don't use this for illegal actions" doens't mean that it wasn't designed for that. i remember back before all of these programs when mIRC was a common way to share files people would post a "warning" about how they are positing all of their music, games and movies for their friend jim to download if you aren't their friend jim then don't download them. That was a lie just to make them try to appear as if there was a valid reason for them to have that stuff online like that. Same here, simplily posting "don't use this for illegal purposes" doesn't mean that their intent from the start wasn't to give people a way to illegally share copywriten material and that they didn't make 99% of their money via people downloading such content.