I recently started a bulk in the new system Hook Nebula (the one Luther "six suns" Nightwish found). I went to ask the ship faction how much I owed and was told "the highest I've seen yet! 5,300,499" (or something really close to that). At the time I shrugged it off thinking it was because the SY was out of system. But it just hit me that that isn't the case. Are the new systems coded as deep space? Or?

For reference, the last highest the person had seen was around 4.3m.

You can see the system's stats on the station detail page. With a RMP of nearly 3m it's certainly well within the possible range, depending on the system stats.

the system is "deep space" since there is no planet to improve the civ-level.
so everything you will start there will cost the maximum.