The current repair system for the tadpole gets rid of the fear of having it destroyed because you never risk losing it, or really have any serious consequences for losing the tadpole.
I think there should be a reapair cost for fixing the tadpole.
I believe the best way to do this is to require all the materials for the base tadpole to repair it. That essentially makes it similar to losing the seamoth in sn1 but without losing all of the upgrades or customizations.
It’s still much more forgiving than losing your vehicles in the first subnautica, while adding an extra risk for exploring around leviathans. And removing the frustration of customizing and upgrading the tadpole again.