It's all a user decision. In the end, a dust filter is just that, a filter. In order to be effective it has to have a small diameter mesh, but also has to have a large enough mesh not to hinder airflow to any ungodly degree. Dust however, isn't all one size, there are microfine particulates that do get through and necessitate the cleaning of a pc at regularish intervals. So dust is going to get into the psu regardless of orientation, it'll collect dust from the pc intakes or the filter underneath.
The difference is the location of said dust. With fan orientation up, dust will settle on the components, especially in a semi-passive unit where the fan runs at minimal times, if at all with the larger wattage units. With fan down, dust will settle on the lid, including the dust filter itself, and will be blown out the rear with fan operation.
Fan down will stay cleaner and probably thermally healthier for its entire life cycle, fan up takes its chances with dust being 'snow-drifted' at heatsink bases, where mosfets are attached, etc.