You are correct that anything we use to carry current does have some resistance due to the physical nature of materials. But in general, the way I understand it, a short circuit means direct connection.
But let's consider a couple cases where we either:
- have an unintentional spike in current due to an accidental direct connection that is considered unsafe to the rest of the system. The current is flowing in a path that we did not intend (hence "short" like short cut) Or,
- would like to connect two nodes in our circuit for a functional reason (a switch)
In the first case, we're interested in the health of our system and a short circuit here means that too much current will be drawn or sunk in a place that we find particularly sensitive - so this can simply mean not enough resistance where "enough" is defined by what our system can safely tolerate.
In the second case, we are interested in connecting two different areas of our circuit together with as minimal distortion/signal/information loss as possible. In this case it is in our interest to have as little resistance as possible.
So I believe to answer your question, it is a matter of context and what you are trying to protect or accomplish. At the electron level, it's just current.