Are you sure they are caps and the short is across the caps?
What kind of short is it and how did you find it? Did you notice device sinking too much current or do a diode test in both directions across the supply rails, or do a resistance test in both directions? You should take (and show) measurements if you are unsure.
If they are caps and causing a dead short across the supply rails that shouldn't prevent you from confirming the device is working after the offender is removed. If they are just used for a bit of supply filtering the device will operate without them especially when testing with your own bench supply (current limited).
As for working out what capacitors, you can deduce it by the surrounding components such as two capacitors in parallel can be the same values. A capacitor next to a regulator could be a nominal value shown in the regulators datasheet or found in comparable circuits.