I don't think it hurt they show, per se, but to be honest, I am very torn.
I miss Zack-Hodgins scenes, mainly because of how cute they got when they were all hyped up about an experiment, or being King of the Lab.
Zack was very amusing, and also very rational, which I think made it easier for Brennan to form the bond with him that they had.
I don't know why they thought removing Zack would be beneficial to the show in any way, especially to Hodgins' character.
I always thought he was at his best in 2 situations:
1) When he was with Zack/King of the Lab,
2) When he went off on his conspiracy theory tangents (adorable).
Seeing as how he still has both, in some way, as he eventually began using the term king of the lab, it didn't do too much harm.
I guess I just absolutely loved Zack, and wish he could come back.