You're compairing first week sales for VLR with life time sales for 999. Here are the most recent Famitu numbers:
3DS: Zero Escape: Virtue's Last Reward - 7,890 / 17,913
PSV: Zero Escape: Virtue's Last Reward - 6,133 / 15,454
NDS: Zero Escape: Nine Hours, Nine Persons, Nine Doors [Chun Selection] - ?? / 4,714
NDS: Zero Escape: Nine Hours, Nine Persons, Nine Doors - 16,967 / 39,653
VLR still sold less at retail, but the gulf is much smaller and it was available digitally. And keep in mind a lot of visual novels don't break 10k, so even while the Zero Escape games presumably have higher production costs due to the puzzles, these are probably still fine sales figures for both games.