I'm not talking about licenses. The fact of the matter is that Runescape is a copyrighted game, and as is every scrap of game code. By loading RS into RAM through a client or program that is not approved or owned by Jagex, that is breaking their Copyright, regardless of the license differences.
The fact of the matter is; that Jagex DOES have the power to shut them down, just as they almost did to Swiftkit before Swiftkit agreed to sign an agreement. The reason they don't is because for every site they shut down, another one will take its place. Think about Kbot, Kbot was sued and shut down, and other Nexus sites rose back up from its ashes. This goes along with the reason why Jagex waited until after they permanently nuked reflection to make the final movement against Nexus. They knew that once they sued and took down Nexus, they wouldn't have to worry about other reflection bot similar to Nexus rising back up and replacing it.
There's really no point for Jagex to waste good money on suing and shutting down sites that will just have imitators shortly after. Think about how long the court case between Jagex and the Snellman brothers lasted. Imagine if Jagex were to go through that process for EVERY single cliented bot? They simply don't feel like spending so much time and money on something that would only be a temporary solution. Even if they shut down all the cliented bots, more will rise to replace them, and then it's the same shit all over again.
Also, it wouldn't take down EVERY bot, just every bot except for Simba, Scar, and RiD, since they don't provide a download for a client that is specifically designed to load RS. The worst that could happen to Simba/Scar is them go after specific script developers, but we all know that Jagex doesn't have the time, nor will they waste the money, to go after a single scripter at a time.
The point is, they have the ability to sue them, however, realistically, it isn't going to be a very efficient use of their time or money to remove something that will quickly be replaced soon after. This is probably a good reason why they're launching the next series of Bot Nukes with Optimus; it's easier to repeatedly nuke ALL of the injection bots at once, than go after each bot site individually to take it down. Make sense?