equill, no i got what you meant. picturing the intake fan in the same location as for exhaust, you will be forcing hot air from the top of the case down through the case, regardless of how cool the outside air is, you are working against physics to push the hot air generated at the top of the case down through the bottom. Since dust generally is stirred up in the air and settles downward, pulling air through the top will also pull in more dust. Therefore, I doubt the flow direction of dust-infused air will matter much.
Now if I follow what you are saying now, I take it you mean to install the intake fan near the bottom vents. That is certainly preferable, but somewhat challenging. I suppose the fan could be mounted parallel to the metal chassis over the large opening behind the FDD above the logibcboard. This is similar to the Classic/II fan with the air scoop drawing air in from beneath the case. I would still seal up the back of the FDD to prevent airflow through the bulk of the drive as well as the other openings in the chassis deck to maximize the draw of cool air through the bottom vents and minimize hot air recirculation. But trust me, you'll still be drawing air in through the bottom vents and my 512Ke that had used a Kensington System Saver had a thick carpet of dust coating the logicboard. That more or less confirms an equal amount of dust is likely to cover the FDD, regardless of which direction the air flows.
None of this is particularly destructive either. As long as we're making changes, I had always thought mounting the speaker on the analogue board face down on the chassis would improve the speaker sound by sending it unobstructed through the bottom vents. With the addition of a fan, it could be mounted face up through the front top grille opposite the analogue board.