Remember that anaerobic bacteria will also live in your substrate, so bare bottom might be good if you have adequate filtration running at say 6 turnovers per hour, but if you keep up an appropriate (or borderline nazi like myself) cleaning routine then you won't have any problems with sand.
If you use river sand you also won't notice feces on it, and if you're running high filtration there won't be any problem whatsoever.
Regarding fish being confused, I'd also be a bit worried if I had pitch black or some strange colour below me where I usually had sand, would give the false feeling of depth, and for bottom dwelling species I can't imagine that being excessively healthy or reassuring, even if they do learn to cope.
Also keep in mind that I keep a number of eartheaters, so my opinion is biased in both the sense that my fish should have sand to sift, as well as them being fun to watch when they do have sand to sift. It's always reassuring to watch a fish sorting through sand for food as it means they have a healthy appetite which is always a good sign.