I'd go w/ scenario 2, why?
1. Since they would have no hiding places, the sand might help them to feel a little more secure, something to lay on/burrow into a bit
2. Loaches like to dig, kinda like dogs I guess, I dunno - but they seem to like it... so I have a colony of small snails in my 30g, every few months I pull as many as I can get out of there and dump them into the 125g w/ the loaches. During the day they dig them out of the sand, little loach treats, plus its live food so its really good for them!
3. IMO, barebottom tanks are kind of, boring. If they are being used for quarantine or breeding then I could understand but main tanks w/ no substrate? I dunno - to each his own, I just prefer the substrate.