This matchup is so rare that its almost not worth discussing heh
but if I had to take a guess it would be a heavy disadvantage or disadvantage for samus . Sheik is a really underrated character in general but she can exploit samus' weaknesses sooo well. She is one of the best characters at approaching through our spam and her dmg outputs at close range are much larger than our own in the long run. We actually have decent kill percent on her though, but she is also harder than most ppl expect to hit offledge, and is really good at swatting us away when recovering and then using her chain to edgeguard when we are forced to screw attack to recover, her aerials come out so quick they are hard to counter, and she combos samus well with grabs/ftilts/aerials. I remember a video awhile ago with rohins facing a shiek (gimpyfish), and I know its outdated and obviously things have changed since, but watching it you can see that samus is forced into a really defensive state and sheik is really constantly getting through and attacking her, and even getting out moves during our initial animations of our moves, and I wouldn't be sure how samus could reliably turn this towards her favor consistently. I know this is sorta similar to how sonic deals with samus too. Anyways here is the link to that
http://www.youtube.com/watch?v=r-ri3CgnSYg&feature=related. (and I know this isn't a really great vid of you rohins I'm sorry
)
I've played some decent sheiks myself and it is very hard to pull off wins then, I can only imagine how hard it would be vs. like Armada or some other high level tourney sheik. We lack the ability to space well against her.
So yea I'm going to say heavy disadvantage- meaning that a high level sheik will beat a high level samus due to advantages that samus can not reasonably overcome. Yea its not as disadvantaged as, say, mk but I still expect that sheiks will be able to beat samus pretty consistently. I could be wrong obviously though, but I get that feeling.