As it stands now you're pretty much screwed if your supplies run out while you are far from a source. The game doesn't really acknowledge that fact mechanics wise, though. Your supply consumption can easily go up dramatically without you noticing, leaving you dry. It would be both convenient and noob friendly it supplies would be handled smarter.
I though about just progressively decreasing max supply consumption once you're below a certain threshold, determined by you maintenance cost. Repairs and CR regeneration would of course be slowed. A warning about low supplies seems to make sense here, too.
Once you only have left enough supplies for a couple of days repairs and CR regeneration could completely stop. Maybe the best way to implement that would be to automatically switch on the "suspend repairs&recovery" button for all ships. Then you could deactivate it manually if you want to keep repairing certain ships, like your flag ship.
Would work as a simple threshold trigger too, without the progressive reduction first. That would give more control, but less warning.