You can read about EVs here. Basically they are extra hidden points that you get by battling. When using Rare Candies, you don't gain any of those points, so your Pokemon could be weaker.
However, if you have trained a Pokemon from a low level up to level 50-60 you will probably already have all possible EVs, so using Rare Candies doesn't matter.
In most games there is a character you can talk to who gives you an effort ribbon, they usually say "this Pokemon worked really hard!" That means you have all the EVs. I'm not sure if there is someone in Sapphire or not.