Problem 1: Spamming
Projectile spam will not help you in this match-up. You need to approach fairly quickly, (unless you are charging your neutral special) which isn't match-up specific, just a Samus thing. What your projectiles could be useful for is approaching - they force your opponent to reflect, shield, or jump. Of course, you should anticipate a reflection with a spot dodge, but not before you've managed to get a little closer to your opponent.
Dealing with Dark Pit's arrows isn't the easiest - parrying each one is probably your best bet, though. You might want to practice this some.
Problem 2 - spacing
Ah, Pit's side-b. The bane of life.
No really, it can be super annoying. Still, zair is a good option, especially when fastfalled. Predicting when Pit will use Side-B is half the battle - it is very punishable.
A good strategy might be to come in carefully with zairs that don't actually hit your opponent, but do keep them at bay, and too close to arrow-spam. Patiently wait until they close that last little gap with an attack, then shield (hopefully parry) and you have your opening.
Problem 3 - reflectors
This one hurts, too. However, you can use it to your advantage. By shooting some obvious projectiles (rockets) as reflector bait, you can sometimes run in and take advantage of the reflector's very long end-lag. Maybe rocket-> down-b roll in -> grab?
You might also want to have a counter-pick for this match-up, since it is unfavorable.