Probably because they don't have a reliable way of differentiating one strand of the double-helix from the other, so matching bases are considered to be a single unit so that it doesn't matter how you've got the pair rotated.
I imagine this could be solved by ensuring that every helix starts out with something like a byte order mark that would distinguish the two strands reliably.
Storage density could be further increased by a constant factor if more kinds of bases were used, or if they could use single-strand DNA/RNA instead (which would probably require some chemical means of ensuring that a free strand doesn't accidentally bind to something else).
I imagine this could be solved by ensuring that every helix starts out with something like a byte order mark that would distinguish the two strands reliably.
Storage density could be further increased by a constant factor if more kinds of bases were used, or if they could use single-strand DNA/RNA instead (which would probably require some chemical means of ensuring that a free strand doesn't accidentally bind to something else).