Has female genital mutilation been an old and common practice in history? If so, why did Allah not make it explicitly Haram in the Quran?
There is historical evidence that some people practiced it in ancient times. I'm sure you can find some reliable historical sources on this subject using the Internet!
(It is good to avoid the temptation of making generalizations about the past, people have lived in many places for many thousands of years, and in many cases we have little or no written/archaeological evidence about how they lived. What can be said is it is recorded or alluded to in some places.)
Many things are not discussed directly in the Qur'an as much of the Qur'an is about general principles and not specifics. The Qur'an also does not discuss male circumcision. Perhaps one could apply the general principle of not causing harm.
There are some Shi'a hadith indicating that circumcision is for males only and not for females.