Not the (great) "Little Wonder" 12 V model.

We have a"sediment" and the pre-filter on the unit itself. Therefore we may be subject to a bit more salt water in front of the unit then you have.

Notwithstanding that, I've found that if you fresh water flush the unit (with chlorine free product water), then you have more days before the stale smell/teaste that needs to be washed out of the filters. It's not that you can't "flush it" by running the unit, it just takes longer. If we don't fresh water flush and leave the unit sitting for more than a week, we get the "swamp" smell and then, you have to flush for a while, or run it through a pickling solution to clean-out the filters.

Your unit may not have this situation; however, if you do fresh water flush before you shut-down the unit, I'd just let your nose and taste buds guide you. If you don't, then I'd certainly think your approach makes sense.