as difficult to comprehend the answer may sound, it is best to deal with your opponent before Mutalisks come out.
but to answer your question correctly, Mutalisks are common in ZvT. learn the timing and prepare accordingly when you think you should. that is, build Missle Turrets at key locations, such as your mineral line or Starport and high-Tech buildings. if it gets really bad defending Mutalisks, build a few Thors and situate them along with your static defenses.
the issue here is pretty much a matter of initiative. if you attack first, he will have to use his Mutalisks to defend. however, if he attacks first with his Mutalisks, you will invariably be stuck using a large percentage of your army to defend, also.
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