A gundam theory
Nano laminate armour is not as invulnerable to beams as we think
For starters, we have only seen it attacked by a long range beam cannon, it may not get off so easily at point blank with a beam saber.
Secondly, beam technology development was obviously stunted during the calamity war and therefore it may not stand up so well to higher power beam weapons such as the hyper impulse beam cannon from gundam seed/ seed destiny, the buster rifle from gundam wing (I doubt there would be anything left if the full power of the twin buster was used on i), the satellite cannon from gundam x or the beam magnum from msg UC, the later can destroy MS with the beam bearly touching it.
To conclude, we don't know how vulnerable the nano laminate armour is to beams, however it's probably not as invulnerable as we all think