There is no issue with the optic after they take it apart and put it back together. It's exactly the same as when it left the factory the first time.
It tends to take at least 3wks, but I have had one take 6.
Whether changing to a different reticle is worth it to you or not is up to you. The VX2 isn't an expensive scope, and replacing the reticle can be more than just a small fee, depending upon which reticle is chosen. I'm not sure if they even offer this for the VX2's - they claim they only do custom work for models offered as custom shop items, but I believe that may be flexible. If you were to choose a mil-dot reticle, for example, it would cost you on the order of $160 +S&H (just got a VX3i back with this change done). Some reticles are only ~$65. If you have trouble seeing the reticle in low light, and the price is worth it to you, spend the money and do it.