There's a guy in my region who thinks Samus/Pit is like 20:80 or something LOL. I think he's nuts, but I wouldn't be surprised if Pit wins this matchup. Keep in mind this is largely theorycraft based on relatively little experience; if Sharkz or Gallo or a notable Samus contradicts me, feel free to go with them.
I can imagine getting down is a nightmare for her in the matchup (and indeed, the guy I mentioned basically ragequit after I juggled him for 100% plus a stock, though he wasn't using every tool she has to mix up her landings--the real Samus in our area I only barely defeated the one time we played). Pit has the mobility to avoid her projectiles, alongside his massively-buffed reflector (though as we all hopefully know, reflectors are more of a convenience than a real answer versus Samus), so I'm not sure what she does for zoning against Pit.
One advantage Samus does have in the matchup is that she's so heavy that Pit can't really combo her out of dthrow before she is able to just nair him. Because of this, I prefer uthrow in the Samus matchup. Combine that with her powerful CC game and I could see her doing decently in neutral, outside of the projectile stuff I mentioned.
In terms of offstage game: the threat of arrows makes bomb jumping a bit of a scary proposition for Samus. If Pit gets to the ledge before she can reel in her tether, she goes into a ton of lag, and if she's far enough offstage to be relying on tether to get back she will probably die to ledge hop back air if she gets hit by it. Lastly, if Pit can force her to land on stage with upB, that should likewise be a hard punish if he gets the back air. That said, usually Pit's gonna be relying on his stellar vertical game for punishes if I'm reading this matchup right, so it comes up less than you might think.
Meanwhile, a Pit that recovers low can be threatened by ledgehop aerials, or by dropping bombs in front of the ledge. Level with the stage, and Pit's asking for missiles or charge shot (he might be able to come down with shield but that puts him low). Arrow harassment will throw them off if they try to go to the ledge, since it'll force them to face front--I've seen a lot of players thrown out of their comfort zone as soon as they get turned around. If Pit's coming high, her best bet is to catch his landings with missiles or CC (he doesn't have aerial answers to CC at all until relatively high percents).
Overall, I suspect this is either a 0 or +1 for Pit matchup, where Samus has a decent advantage in neutral due to CC but gets punished very hard if she gets juggled.