I used to also have a lot of trouble with samus, hopefully i can help shed some light on this.
For missile spamming Samus: I would suggest one of two things.
- To approach her, your nair can eat through her missiles and also provide a mini wall against an attack if she follows up with the missile to attach you.
- The second option would be to rshl->shield. This way you shorten the distance between you and samus, prevent her from spamming missiles as much, and possible lead on your own attack.
There is always the third option of jumping over the missles, however a good samus will intercept you with a nair or she can wait and sheild w/e move you come down with and then upb out of shield.
Also, I wouldn't suggest reflecting her missiles as much. The reason being that she can follow up the missile, jump over it after you reflected it, and then hit you with a dair while you are in the lag from the shine.
As for playing her in general, I recieved some great advice awhile ago from phanna. He suggested that whenver you are not punishing samus for a laggy move with a dair->utilt/shine or something else, that you should laser her. Really, in this matchup, it comes down to your lasers. He also suggested that dtilt after a jab is good for a kill, yet you shouldn't use it as much when fighting or they will catch on and punish you.
Hope I was able to help out.