No, of course Apollo didn't see the raider. He would have reported to Adama had he seen a raider when Kara's ship blew up, this leaves him thinking she was just breaking under the pressure.
But, RDM did not say the
viewer did not see a Raider. He said Apollo didn't see it.
Later in the episode we see the camera outside Lee's viper as he's talking, before he sights her the raider flies away from her ship.
The raider existed, he just missed his opportunity to see it, he was too busy paying attention to Kara's ship and the raider flew the opposite direction. Why would they bother showing the raider from lee's point of view if not to show it was real? Besides, we know she's not gone for good, and she can't be a cylon (she had a mother that killed toasters in the first war? HELLO? she's NOT a cylon). So that means the ship must have helped her in some way.
And those are definately bullets that hit her cockpit, they were blue tracers, particles in the atmosphere don't look like tracer rounds.