I'll start by listing general ways of dealing with missiles.
1. Ice blocks can go through missiles. If you full jump ice block when Samus shoots a missile, you can have one ice block intercept the missile and the other one continue towards her. This is risky, though. If Samus land-canceled the first missile and immediately shoots another one afterwards, the second missile might hit you. Also, the ice blocks might fail to stop the first missile if it doesn't hit it a certain way. It's still worth keeping in mind, though.
2. Wavedash -> fsmash through missiles. If you're close to Samus and she shoots a missile, whether she's on the ground or in the air, you can wavedash fsmash such that Popo gets hit by the missile and Nana gets through and fsmashes Samus. This is extremely good at low percentages.
3. Use platforms! This might be kind of obvious, but it's worth mentioning since you can frequently avoid missiles easily by just letting them pass below you.
Some ICs don't like FD against Samus since it makes coping with missiles harder. She probably wouldn't take you there since she still has better CPs, but you might want to consider striking/resetting it against her first round, which is something you wouldn't do against almost any other character.
Regarding recovery, try to recover really high against her, at least on stages with platforms. It's way to easy for her to hit you out again if you don't. Actually, you'll still probably get hit even if you recover high, but you'll probably be able to make it back afterwards unless your DI is bad.
Other miscellaneous notes:
-You can't punish properly spaced and timed jab-cancels into your shield, regardless of which way you're facing. Your best bet is to roll or maybe wavedash away at a time that she doesn't expect it.
-If the Samus is just sitting by the edge looking for an opportunity to dsmash you, feel free to stick to platforms or the center of the stage. You don't have any obligation to approach her. You actually can punish dsmash easily with wavedash OoS -> grab, but I don't like putting myself in a position where she can dsmash me by an edge since Nana is almost guaranteed to die if you get hit
-Ice blocks are really good in general against her. She's a floaty character that doesn't move that fast on the ground, so it isn't easy for her to punish ice blocks.
-It's easier to KO Samus off the top than off the sides, but you can still KO her off the sides. You can sometimes edgehog if you think she's going to try to sweetspot the edge with up-B. Also, it's really hard for Samus to get back on stage against ICs. You can harass her with ice blocks (synched or desynched) pretty well when she's trying to get back to the stage. Once she's on the edge, it's hard for her to get around desynched blizzards and ice blocks spaced such that blizzard doesn't quite the reach the edge, but there isn't enough space for Samus to stand on stage without getting hit by it.
