Yes, i would definitely go with the 2000Ah 2V batteries (as long as they are from a reputable manufacturer). Using the single cell (2V) batteries means you will only have 1 string of batteries.
When using 12V batteries you can have lots of issues with battery balancing in multiple strings.
The 24 x 2v, 2000Ah batteries will create a 48kWh battery bank. However you should only discharge 30% on a daily cycle so 16kWh usable capacity. With the conversion and inverter losses this will be approximately 14kWh.
Wondering how do you use 3kW per hour over night? That is a lot of power! Over night that will add up to 30kWh?