The concept of recoil has existed since Gen I, so it definitely existed in Gen III. Take Down may have been revoked of recoil damage because the user of the recoiling attack may have had the Magic Guard or the Rock Head ability. Rock Head prevents recoil damage specifically, but Magic Guard prevents all kinds of indirect damage, including recoil.
As I look through the Pokemon that know these abilities, many of them are available in FireRed and Emerald so your observations may have just been of Pokemon with one of those abilities. Otherwise, you may have just not paid full attention or the recoil damage observed may have been minuscule or something.
Hope I helped. :)
+ Serebii Abilitydex