All of my bikes have naked cables. The only problem I've noticed is that the little donuts don't always keep the naked cable from wearing the bike's paint job. But then, the spots that have housing have worn the paint a bit too, so I don't know if that's significant.

I was a bit perturbed at the wear on my gold Waterford, so my LBS put a thin light sleeve over the naked cable that concerned me the most. Not quite a housing, more like a very thin drinking straw.