You are correct, as you increase capacity, the Latency increase as well. For example, the lowest Latency I've see on DDR3 is Cas6 but DDR2 goes down do Cas3 (DDR2 400). This seems to be the nature of the best. You are better to run with lower latency than you are with higher MHz.
However on the flip side, higher capacity memory gives you the ability to "underclock" and run at tigher timings than you might be able find for DDR3 of equal speeds. Example, G.Skill PI 6GB (3x2GB) DDR3 1600 set runs at Cas7, however the G.Skill Tridents 6GB (3x2GB) DDR3 2000 set runs at Cas( but can be "underclocked" to DDR3 1600 Cas6, which is out performs the PI model.