From a historical perspective I think ebony was not usually used for the darker squares in chess boards. It was an expensive wood even for the time, and as you say it has a tendency to hide the black pieces.
The sites will recommend whatever they think will sell best, and there are lots of people who care more about the exotic value of a chess set than the playability, hence all sorts of unsual combinations.
In my own opinion, 3 colored chess sets tend to be the best looking and the best playing. I play with boxwood and shesham (brown) pieces on various natural and black boards, and I think it is a very clear combo.
Some links you may find interesting:
http://crumiller.com/chess/chess_pages/boards/JaquesAntiqueBoard.htm
http://crumiller.com/chess/chess_pages/boards/Jaques39thSetOnLargeBoard.htm
http://crumiller.com/chess/chess_pages/staunton/JaquesStauntonShippingSet.htm
http://crumiller.com/chess/chess_pages/boards/JaquesAntiqueBoardWithInsurancePlacard.htm
As you can see there were several combos.
If it were me buying a set I would be going for the boxwood/mapel&walnut or boxwood/maple&mahogany combo.
An Ebony and Antique Boxwood chess set.
Would an ebony squared board have tendency to hide the black pieces? I saw one site today recommeding their ebony square board to go with their ebony & boxwood set.