High-energy Li-Be-B nuclei in cosmic rays are being measured with unprecedent accuracy by the AMS experiment. These data bring valuable information to the cosmic ray propagation physics. In particular, combined measurements of B/C and Be/B ratios may allow to break the parameter degeneracy between the cosmic-ray diffusion coefficient and the size of the propagation region, which is crucial for dark matter searches. The parameter determination relies in the calculation of the Be and B production from collisions of heavier nuclei with the gas. Using the available cross-section data, we present for the first time an evaluation of the nuclear uncertainties and their impact in constraining the propagation models. We found that the AMS experiment can provide tight constraints on the transport parameters allowing to resolutely break the degeneracy, while nuclear uncertainties in the models are found to be a major limiting factor. Once these uncertainties are accounted, the degeneracy remains poorly resolved. In particular, the Be/B ratio at ~1 - 10 GeV/n is found not to bring valuable information for the parameter extraction. On the other hand, precise Be/B data at higher energy may be useful to test the nuclear physics inputs of the models.