When I read the book in my youth, I remember being surprised not only by the lack of muskets, but also that it was more about D'Artagnan than about the titular Three Musketeers.

Anyway, if you think about it, it makes sense: muskets were a new and unproven technology that still needed a lot of development to actually become usable firearms. While you were busy lighting the fuse on your musket, your opponent could attack and kill you with his sword. So, of course, the king's elite troops needed to be equipped with these "high-tech" weapons for prestige reasons, but due to their impracticality, it's not surprising that they didn't actually see much use...