I think the best way to keep your models clean is put them in sealed glass/perspex display cases. After years of dusting my models and seeing the windows get dull and scratched I invested in some clear plastic cases which protect the models just like the box does.
They aren't cheap (especially if you have lots of models ), but they help show the models off and stop them being ruined by dust and dusting.
So, as soon as I buy a new model, it stays in the box until I get a case for it. It also looks cool because rather than having them stuck on a shelf, I mount them at various points on the wall and they look the nuts and it makes viewing and showing them much easier. The amount of times other models got dropped by butter fingered friends makes the cases well worth the investment.