Will changing my MAC address void my warranty or affect any existing programs? Noobie here 
Pretty much what the title says.

I have 2016 Macbook Pro (macOS 10.12.3), so, will changing the MAC Address by terminal or by using some program like SpoofMAC void my warranty or AppleCare Protection?

Will it hinder my iMessage or Facetime or any other existing programs?

Thanks!
It shouldn't. I'm currently doing it on hotel wifi and everything seems to work fine. Restoring your default MAC address is as simple as rebooting the machine, so no way for Apple to really know anyway!