It's not up to the FBI, it's up to the DEA and FDA. The FBI has to follow federal law and as long as that law says cannabis is a schedule I controlled substance there's nothing they can do about it.
Well, obviously the FBI can't encourage its employees to smoke pot, but unless there's a federal regulation on drug testing, the FBI isn't forced to drug test it's employees.
It’s always up to law-enforcement, which laws they want to enforce.
Some laws are harder to enforce than others too. That’s why people drive around my town with really loud engines and the cops never do anything about it.
There are plenty of laws that the FBI does not enforce within the realm of white-collar crime.