6v GC batteries are made for deep discharge time and again. They are built heavy to deal with it. They will last longer.
From an electrical standpoint 1 series string of batteries is better than multiple parallel strings. Parallel strings rarely charge and discharge evenly due to differences in the wire length, terminal resistance, battery internal resistance, etc. 2 6v in series will always charge and discharge evenly.
If you're checking and replenishing water 2 12v will have 12 caps. 2 6v will only have 6 caps.