Maxwell has a 63farad rated for 125vdc, max current 1900A that weighs 61 kg. ([datasheet] http://www.maxwell.com/images/documents/125vmodule_ds_1014696-7.pdf1 Heavy).
Heavy, but does exactly what you want, with no DC/DC sitting between capacitor and motor. You
You can put your batteries in series to get 48+48 = 96 volts. You
You can put capacitor in series to get 48+48 = 96 volts.
Downside
Downside, capacitance cut in half. Or
Or keep the batteries at 48vdc, and use the DC/DC converter to limit the current draw from the batteries and recharge the super capacitor bank. Or you could select a motor and controller that runs on 48vdc?