The Narada's weapons are from the future and it was expected that they'd go through the older shields like they "were not there" as seen in the movie.
As to the TOS Enterprise firing phasers to knock down incoming missiles I forgot to list "Balance of Terror" where they fired at the last second to detonate the Romulan warhead. That same episode suggested a phaser strike against the plasma weapon as well to detonate it. We've also seen the E-D take out a Ferengi missile that was fired at the Barzan wormhole (IIRC). Oh, and in TMP, the Klingons tried shooting down V'ger's energy weapon with their own photon torpedoes.
What we've not seen though is an explicit defensive phaser fire against incoming photon torpedoes. Perhaps photon torpedoes are too difficult to destroy with phaser or disruptor fire? Wasn't there an episode where they fired photon torpedoes into a star and the casings protected the warhead up till when it was needed to explode?