Is it viable to boost capacitor voltage to improve energy density?
In short: no.

To use some current Digikey parts/prices and the 50J storage requirement for just the capacitors:


50J using nominal 50% discharge of a 5.5V supercapacitor (no derating) requires \$\frac{50J}{5.5V^2 - 2.75V^2} \approx 2.2F\$


The PHV-5R4H255-R from Eaton is rated at 5.4V, 2.5F, and priced at $11.90 quantity 1 on Digikey.
There are a variety of other supercaps at 5 to 5.6V and capacitance from 90F to 10mF

50J using nominal 100% of a 2.5kV ceramic capacitor (derate to 2kV) requires \$\frac{50J}{2000V^2}=12.5 \mu F\$


The 3640WC223KAT9A from AVX is rated at 2.5kV, 0.022µF, and priced at $4.448 quantity 180: total cost of 568 capacitors is $2526.464. (!!)
Prices don't get much better and capacitance doesn't go up, but other ceramic capacitor can be considered



So, you might gain an exceptionally low ESR from having many ceramic capacitors, but they will be a challenge to assemble hundreds of components. Very specific pulsed applications may gain an advantage from chip or chassis-mount, high-voltage ceramic capacitors. However, for backup power in electronics, supercapacitors will have a much better value and energy density in comparison to high-voltage ceramic capacitors.