Repeatedly farming an area question

Does farming the same area repeatedly, after long durations of downtime, still stack the effectieness decrease penalty?

For example, if I farm a zone twice, logoff, and come back several hours later (Or even a day later), and proceed to resume farming it, does the penalty keep going up or does it reset during that downtime?

There is no stacking penalty that I know of. But there is a drop rate penalty that has to do with the difference between your level and the level of the area. See the drop rates section of the mechanics thread for more info.

There's no penalty at all for farming an area many times over again.