To be clear for future readers, Vitamins do work on level 100 Pokemon. What doesn't work are the EVs gained from defeating Pokemon in Gen 3 and 4 (as this is coupled with experience gain in those games, and level 100s don't gain experience).
This means that you need to max your EVs before level 100 in those games, because if you don't, then you can only get EVs from Vitamins, which have the "first 100" limitation.