Spam-Samus is tough; I'd defer to Bringer because my crewmate dropped Samus awhile ago. You can duck under most missiles if they don't get them low, so definatly use that to your advantage. SH Dair is a reasonable approach, it'll beat out her sex kick. Juggling is pretty much limited to eggs and chasing her around with upsmashes, because her D-air is pretty beast and her bombs are fruity.
Samus also has your crappy grab and a slow air game so while she's in the air, use your wavedash to position yourself and then try to roll behind her for the downsmash.
Edgeguarding Samus is sooooooooo fun. If she tries to bomb recover, you can do about 30% worth of damage with eggs and aggravate her by zerging her bombs lol, but that probably won't kill her, and the real fun comes when she's trying to sweetspot.
Samus has two options for recovery: Grapple, and Up-B. When she's close to the stage, she's probably just going to up-B. Basically if you get the idea that this is the plan, start dtilting as a mindgamez, then instant edgehog her, and immediately roll up and forward smash. Mostly you'll get the kill off the edgehog.
If she triest to grapple, IH her again, because she'll likely go after the sweetspot. This time just do a ledge stand, and crouch cancel her attack into a down or upsmash, whichever you feel is appropriate, and go from there. Not 100% foolproof, but most Samuses will hop up with a forward air or neutral air and you can CC both just fine. You can also dtilt her out of her rising grapple and do the Instant-hog->smash just fine, and if you're confused, just go for the dtilt.