Hmmm, I don't really agree with some of the advice here.
Hylian Shield only works at a distance and doesn't get you anywhere offensively.
Powershielding? Come on, you don't really expect to use that effectively?
Out spamming? It's not about "out spamming," it's about using your projectiles effectively.
Yes, I expect to. It's great when they fire them pretty close range, becuase they DON'T expect it to come back. If you're early, you have your shield up, if you're late, oh well it hits your hylian shield. I do powershield missiles sent at me often, and it's great to see Samus charge face first into it. My brother is more careful about shooting off missiles close range now because of this.
I can relate to this situation because my brother has perfected intercepting me off the screen. His missiles are pretty much calibrated to Link's fall speed so I need to find ways around them anytime I recover. His "projectiles thrown" total used to be nearly 180 after every five stock match.
As mentioned before, bombs are sexy. Remember that they'll defend you from both missiles and charge shots. Pull one out if you're nervous about the charge shot. Boomerang works best for missiles at any distance though. Just lob it at her and try to keep it in front of her, even bounce it off the floor to keep it in missile range longer if she's on the ground.
Grounded arrows are pretty useless. It's great if the Samus doesn't know about that just to piss them off, but I've tried to lay a barrier and gotten nailed by the shot numerous times because it just takes too long. Only do it if there is A LOT of distance between you, and then probably use it as a shield to pull out a bomb. Remember, a well placed jump can put it over the arrow (and your hylian shield. I've even had it go UNDER the shield on flat ground).
Nair is quick and will stop a missile if you're bound to hit it. You can just short hop nair through them if you want, just don't let them get under your foot or it'll nail you.
Overall, just spam the boomerang to take the heat off of missiles and to try and put her where you want her, but lay off of it when she has the charge shot. You will be punished for boomerang spam when it gets eaten by charge shot.