The sensitivity in measuring one effect is no guarantee it will measure any other effect.
As far as I know neither of the Voyagers is fitted with an atomic clock so this measurement method does not work on it.
According to the article dark energy signatures would be evident in slight time shifts. Slight as in in the range of "billionth of a second". Light travels 30 cm (1 foot) in that time.
According to the article GPS satellites can measure those. They just don't check if there is a pattern to them. That pattern would indicate the presence of dark matter.
GPS satellites have Cesium clocks. Those are accurate to one second in 1,400,000 years. That means the error the article is talking about is the error the clock naturally has over about half a day. Apparently that is precise enough.