I dont beleive question cant be answered to the 100% with the information you give. I suggest you experiment to find out on a single mac, with a time machine backup before deploying. The effects it has depend completeley on the application and the canges you apply.
As far as my experience goes I've just modified the Dock application in order to alter how exposé looked by replacing two images in its resources. I suffered from no instability, but again, it was just 2 images.
About software update, it is possible that the changes are overwritten, but again, it depends on what you are modifying.
Why are you modifying CoreServices? I suggest other methods to achieve what you want to do, but if its the only way, Time Machine is your friend.