If the body of the Tzadikim do not decompose, even over many years, why is Yosef HaTzadik written "the bones of Joseph" and not his body?

That idea, as most midrashim, does not necessarily apply to every single righteous person who ever lived. There are documented testimonies of tzaddikim whose bodies did not decompose, most notably Eliyahu Hakim and Eliyahu Beit-Tzuri who assasinated the British anti-Semite Lord Moyne, were hung, and whose bodies were brought to Israel only after 30 years (testimony of Prime Minister Yitzchak Shamir), and the grand rabbi the Chida whose body was brought to Israel after 150 years (testimony of Chief Rabbi Rav Mordechai Eliyahu), but they are the exception who testify to the rule.