Hi,
It is difficult to answer this question very generally. But sometimes basis set superposition errors (BSSE) can be significant leading to an overbinding, i.e. too large binding energy. If you get very different binding energies with and without the Counterpoise correction, it is probably important. In order to address the problem for a particular case, I would suggest that you try to compare your results with plane-wave calculations, using the PlaneWaveCalculator, since this does not suffer from BSSE.
Regards,
Troels