I think without actually seeing the evidence of your concerns it is very dificult to make any kind of judgement, I and a few others have mentioned photos, what was agreed in the quote etc., which you haven't really addressed in your replies. It is not uncommon to drill holes of that size through joints for the reasons already stated by others, I appreciate that you are questioning how they have been drilled. However we can't knock the company concerned without further information and what you and they had agreed prior to the installation. I totally understand that it can be a stressful time for all concerned and there does need to be some solution to come to a closure that is positive for you.
I think you need to go down the complaints channel and provide a written statement accomanied with photographic evidence in raising your concerns