What is the significance of Salt ending?

Yes, the Director's cut implies that, to the extent that you can call it implied. Almost beats us over the head with it. From an interview with Director Phillip Noyce:

Phillip Noyce is not paranoid, but his belief in sleeper spies such as Evelyn Salt, the title character played by Angelina Jolie in the film "Salt" that he directed, is palpable.

"I do believe that there are tens of thousands of sleeper spies all around the world, not placed to gain information but rather to gain positions of influence. Imagine if, at the highest levels of our governments, there were enemy agents? Just think about if the man with the finger on the trigger is an enemy agent, and what a coup that would be. Essentially, that’s the ending of the extended versions."

"My favorite version is the director's cut extended version, which to me provides the most appropriate ending to the story, because it is an ending yet just a beginning -– and it's an ending that turns the whole story on its head," says Noyce.

_{The "extended versions," of course, reference the film's DVD/Blu-ray [...] Like most of the releases in today's home entertainment market, there are different versions of the film offered, including three separate endings.}

The Director's cut being the one that has the news report at the end. So yes, the President is implied to be a Ruskie sleeper agent.

There is nothing to suggest he's Evelyn's blood brother though. Just another one of the children that were raised as sleep agents.