Can a poorly done second degree ruin one's academic record? Currently I have a BSc degree in Computer Science, and in the future I plan to get a Master degree in Computer Science. In my opinion, my BSc grades are good enough to help me be accepted at good universities in my country. 

Also I'm considering doing a second BSc degree (in Electrical or Mechatronics Engineering), but I don't think I'll have enough time to study in order to get very good grades. 

Could this ruin my academic record? Would it lower my chances of being accepted in a Master's course in the area of Computer Science?
Yes.

I think it is pretty obvious that if you provide the transcript for your second degree, a poor performance harms your chances.  This provides relevant information about your academic ability and/or work ethic, which a graduate program would consider.  It might even be weighed more heavily than your first degree, since it is more recent (and in a relevant subject to your planned masters').

So the question becomes can you just not tell graduate programs about your second degree?  I don't think this is a viable option.  A graduate program will expect you to submit information about all previous studies.  Not submitting a transcript for a second batchelor's degree will most likely be breaking their rules.  You would likely have to be deceptive in any application, interviews, and discussions with the potential graduate institution.  I think this is just wrong, but even if you don't have any moral qualms about it, you are placing yourself in a very bad position.  There is a chance you could get away with it, but you also might get caught, and that would have serious consequences.