I've been starting to buy from the herb shop in Lumiose city, because the price per HP is much better there. However the description of the "Energy Root" notes that it is very bitter, does this have any negative effects on my Pokemon, or does it not matter?
Herbs are indeed generally cheaper and you also have access to the Revival Herb which is an equivalent for the Max Revive, which you might find more worthy than a simple Revive (which recovers only half of the max HP of a fainted Pokemon), but there is indeed a side effect. These herbs affect the happiness of Pokemon.
According to the last generations, herbs reduce the happiness of Pokemon by a certain amount (contrary to fainting which decreases the happiness points by 1 each time):
Happiness of Pokemon | 0 - 199 | 200 - 255 ---------------------+----------+---------- Using EnergyPowder | -5 | -10 Using Heal Powder | -5 | -10 Using Energy Root | -10 | -15 Using Revival Herb | -15 | -20
Table sourced from bulbapedia and assumed to be similar in Pokemon XY.
What happiness points mean in-game are:
Some Pokemon evolve when their happiness points reach a certain minimum of 220 happiness points. You can see a simple table containing such Pokemon here.
Return and Frustration are moves that are affected by happiness. Return's base power increases with higher happiness whilst Frustration's power increases with lower happiness. Both have a maximum of 102 base power.
From the last point, some might even argue that reducing happiness has some advantages. It's just that it's more difficult to decrease the happiness points of a Pokemon than to increase it.
Herbs make Pokemons unfriendly towards their trainer, the equivalent of having your Pokemon faint many times while battling with it. In practice this means that the move Frustration will have higher power when used by the Pokemon in question, while Return will have less power. In addition, this will make it harder for Pokemon that evolve on friendship to evolve.
Note that friendliness is a different value from affection (gained from Pokemon-amie minigames), and that herbs will not reduce affection.