If it's measuring as a short circuit then it's either shorted, a very large value, or shunted with a low resistance.
In any of these cases a capacitance meter will probably fail to produce a meaningful result.
If it's a really high value you should be able to identify this from markings. If it's a supercap of some sort you would expect the voltage across it to vary verrry slowly from the current of your meter's resistance range.
If it's shunted by a low resistance (maybe an inductor or a short on the board) then removing the capacitor will allow you to measure it's value.
If it's really shorted, none of this will help, but it's hard to tell for sure without disconnecting at least one end from the circuit.
If it is shorted it no longer acts as a capacitor so a capacitance reading won't help you at all.