Can V=IR be applied to a short circuit?
Yes, V=IR can be applied to a short circuit.

The most extreme form of a short circuit is a superconductor. The voltage across a superconductor is zero, regardless of the current flowing through it.

What you can't do is use I=V/R when R is zero, for obvious numerical reasons.

In practice, what most people call a 'short circuit' is just a very low resistance, for instance a spanner or short length of copper wire dropped across a couple of terminals. Here the resistance is finite, so we can do the calculation either way round.

When we are measuring a low resistance, we often use a Kelvin 4-wire connection, to use the V=IR definition, or at least the other inversion of it R=V/I, directly. We set up a current through the unknown resistance, then measure the voltage across the points that we want to define the resistance between. For very short wide conductors, the voltage measurement can get very close to zero.