You're fuzzing the crucial distinction between well defined and narrowly tailored exemptions, which are of course normal, and these exemptions, which are complete blank cheques that effectively neuter the rule they attach to.

No laws are absolute, some laws are more holes than cheese, but a law that says "A government must not punish you for doing X, except in accordance with duly passed criminal laws that make X illegal" is almost entirely pointless. It exists solely to make people feel fuzzy when reading the first half of the sentence, which is the only part you'll ever hear quoted, while not actually impeding anything a government may wish to do to you. This is intentional. Those carte blanche exemptions do not consistently appear across international human rights treaties by some accident.