Well, your foes' stats will be adjusted, as well, so certain Speed Points and Damages you wanted to achieve will be altered, but she will still get the proper boosts from the EVs.
For example (all Pokémon have all 31 IVs), a Machamp with 252 Attack EVs and an Adamant Nature using Brick Break will do a maximum damage of 576 on a 252 HP/252 Defense Bold Blissey, which is 80.7%, at Level 100 (for both). In contrast, if they were both Level 50, Machamp would do 296 Damage to the Blissey, which is 81.8% damage (assuming I did calculations correctly). So it does make a bit of a difference, but the EVs WILL be applied.