The two could's do not mean the same thing.
In She couldn't come, the could is an alethic modal, which refers to ability. So it means 'She was not able to come', which entails that she did not come.
In She couldn't have come, however, the could is an epistemic modal, which refers to possibility. This is Logical possibility, which is based on evidence and logical conclusions from it. Consequently, it means 'It was not possible that she came', which entails that she did not come.
Note that both readings have the same entailment; this is not uncommon.
Every modal auxiliary verb has at least two readings;
- one reading is usually epistemic
This may not be the place. This must be the place. This should be correct.
- the other reading is either deontic
If he will agree, it's a deal. She must see him at 4pm. We should wait in that room.
- or (in the case of can and could) alethic
She can speak ten languages, and could understand Hittite, if it were still spoken.