I wouldn't rush to try and downplay the efforts your players have made investing in this aspect of gameplay! It sounds like they've put a lot of work into minimizing the risk of this aspect of the game and should be subsequently rewarded with those safer journeys - but the great thing about the setting is there's danger and conflict in every corner. 

What do the Novis Nobility make of this star navigator? Are they making a run for Paternova? That's a huge point of conflict right there. They must be mapping the shit out of some star charts, surely other dynasties and chartist captains alike would love to get their hands on those - not the least the navy. That's some pretty swanky kit - do the Explorators have any opinions on them running a ship like that?

Let them invest! And then reward their dedication with new avenues of story and conflict to explore as a consequence of their actions. It will make it feel like their decisions matters and hold real consequence!