Honestly I'd be fine with SH being a kidnapped selunite, it wouldn't be my favorite plot choice but it'd be fine, however I'd hate it if she were from the ruined village. I cannot imagine us coming back to this area, the area itself is given no sense of importance and its only plot hooks so far are ones focused on getting us to leave fir Baldur's Gate, and it feels like its too convenient on top of everything else. We just happen to land in the right place to be in Shadowheart's home town? At the very beginning of the game?
Fair enough

. As I said, it's probably not what's intended at all, so you're probably safe.
Personally I found the ruined village and whatever happened there and at the Shattered Sanctum an interesting mystery and still had lots of questions when we left, and am at the very least hoping to get some answers to as we get to know more about Ketheric who I think was involved, but mileage clearly varies.
As to coincidences, I personally wouldn't find it too much that a hundred years into her life Shadowheart's secret mission to steal a box from the gith led to her being captured by mindflayers on a ship that crashed in an area she'd never have otherwise visited, but includes a village that triggers some buried memories and odd power flares that kicks off a series of events in her personal life that could radically change her understanding of who she is and her connection to her faith. But then I have a reasonably high tolerance for coincidence if it drives (what I consider to be) interesting stories, but of course totally understand others might find that stretches things too far and not an interesting story anyway.
You'll just have to consider yourself lucky I'm not a Larian writer

.