Voyager was the only ship in that quaderant with a Federation warp signal, so it was easy to track. There was an ep. where Seska mentions this as does Janeway when looking for lost shuttles.
Season 3s "Distant Origin" shows another way to track them.
It's amazing then that the Equinox didn't run into the Borg then. The Borg showed up more often because Voyager was had simple gone though their region of space. Each story should be taken on a story by story basis though and not taken as a whole.
Without giving anything away.
Remember what the Equinox was doing?
I assumed what they were doing pushed them well beyond or around Borg space, so they never were detected.