If you use action replay to level up a pokemon faster, the level increase will affect its stats. A pokemon's stats are influenced by:
-Nature
-EVs/Ivs
-Level
-Base Stats
Leveling up your pokemon faster via AR won't result in lower stats, if anything, it'll make them higher. However, neglecting their EVs, having a reducing nature, and low IVs can all result in lower stats for the pokemon though. You can't control base stats obviously. Since you're using AR, you can probably just edit the game to set the pokemon as needed. If you want quick EVs, but don't have a code for it, you could always just use a money code to get the money to buy vitamins (which only give up to 100 EVs in a stat if said stat hasn't already gone over 100.)