They certainly have a higher total resale value. But they don't retain the price gap. On a previous generation used iPhone the price difference on each capacity is $50. So you lose an additional $50 when reselling a 64gb model from the 32gb and $100 from the 16gb.
The best resale value is the lowest capacity current generation. So if you don't need the space get a 16gb model.
Currently you can get an unlocked used 4s 16gb for $350, 32gb for $400 and 64gb for $450 on average. If you scrounge around and are patient you can knock off an additional $50 to $75.