The OpenROV Cockpit display shows battery voltage (that is, the voltage of the input after the two parallel 3-cell packs are combined and go through the blocking diodes), so that can be used to monitor the voltage of the system.
From our experience so far, it seems that the ROV starts to shut down on its own when the voltage gets below around 7.5v (since the regulators supplying the computers, etc need more than that). At this pack voltage, each battery is right at around 2.5v, so the likelihood of going severely below that inadvertently is pretty low when everything else is acting nominally since the ROV won't even run properly.
Additionally, we've started including little inserts for battery tubes in our kits that allow slightly shorter cells that don't have built in protection circuits to fit in our battery tubes (which are long enough for batteries that do have those circuits). These battery adapters have 6A polyfuses in them which will cut off the battery tube if an unusually high amount of current is drawn (i.e. a short occurs somewhere).
We've also been talking about cool ways to build in alerts and housekeeping features into future versions of software. Brian Adams has done a great job making it possible for people to add plugins, so perhaps someone can make a battery monitoring plugin one day!
For now, the LiFePO4 26650s seem to work great. The only issue we sometimes have is that the "positive" terminal does not protrude out enough to make contact with the "negative" terminal of the next battery, so we've needed to add small solder globs to the top of each cell. If you have any easy/ low cost ideas for other ways to get around this issue, please let me know.
Anyway, there are many power management options out there, and I'm excited to see where it all goes.
Good luck with your build!