Samus has to be careful about how she shoots missiles.
Reflected strong missiles can kill at 100%.
CS can heal a lot and if you reflect it, well, yeah, GG.
Approaching from directly above is not Ness' strong point, especially against someone with a ranged grab. When she's shooting missiles in bulk, get in the air.
When you're landing, some Samuses will try to CS it and others will save it.
It's reasonably safe to land just outside of grab range, especially if CS isn't going to kill you anytime soon.
Otherwise FF & Shield or Magnet against the trigger happy ones.
When you're close, try to put pressure on her by waiting. If she's holding shield then you might be able to bait a shieldgrab by weaving in and out of her range or by hitting her shield and putting yourself out of grab range (ex. FH rising Nair)
If she jumps, you can bait out an aerial, PKT juggle, challenge her or punish her landing. I think Fair beats hers. Samus is still pretty floaty.