Use d-air to break through missiles and close the gap between you and her. N-air can work as well, but the hitbox isn't out as long so it's riskier. D-air gives you pretty much complete coverage in front of you and below, so you can just jump towards missiles and sh d-air to break them.
When you're in close quarters, most Samuses will be scared to shoot missiles and either try to escape, poke you with moves like f-tilt and ditlt, or crouch cancel your approaches. If she isn't shooting missiles, you can turn around and b-air which is really useful since it comes out quickly and isn't easily crouch canceled. Samus is kind of like Peach in the sense that you want to keep her at a range where she feels pressured and might throw out unsafe moves. A lot of her attacks are punishable with WD out of shield or shield grab. If she's f-tilting a lot to stuff your approaches, you can sit slightly back and throw projectiles or have Nana blizzard.
Since Samuses tend to shoot missiles from underneath the side platforms, a lot of the fighting will take place near the ledge (which is pretty different than other match-ups where your goal is to retain control of center stage). Her d-mash can be pretty deadly because it turns Nana around, making it impossible for her to grab the ledge, so avoid going in with moves that are easily crouch canceled.
If you can force Samus to jump up above the platform, you can get a lot of mileage out of u-air combos.
