Ra's knowing that Bruce was Batman, and Joker, assuming that Batman had an interest in Rachel is nothing like Blake knowing that Bruce is Batman. That's a stretch.
The bit with Blake is convoluted writing, it's bad, really bad. There's something wrong when you JUST introduce a character out of the blue and make such a big revelation. It diminishes the characters involved especially when the final film is advertised as this far reaching story that connects both, previous stories. If Blake was so crucial, they should have set him up in the other two films . . . oh wait, he didn't exist until 2012.
Ra's knew that Bruce was Batman because it was self explanatory to him. This is the guy that TRAINED Bruce. He'd know his style, his "theatrics", hell, even his gauntlets. It not a big assumption to Ra's, it's obvious. Nothing like, "I saw it in yo eyes".
The Joker? The Joker thought that Batman WAS Dent up until the point where Batman arrives in the Batmobile to protect the convoy. When he was at the party, he was there for Dent. There WAS no Dent. So he assumes that Dent and Batman are one in the same. Everyone in Gotham knows that Rachel and Dent are an item, so obviously the Joker does too. That's why abducting Rachel was a sleight of hand, a secondary plan. Once he figures out that Dent ISN'T Batman, he has an advantage.
That's why he goes from wanting to kill Batman outright to not wanting to kill him. At first he thought Dent was Batman, who he also wanted to eliminate. Dent loves Rachel. Joker assumed that Dent was the one that threw himself out of the penthouse to save her (because he wasn't there). So it's all plausible.
No way is that anything like, "I KNEW WHO YOU WERE CUZ I'M AN ORPHAN AND I COULD SEE IT IN YO EYES".