They will not do much damage and will likely not count for the owner's overall damage (Yet to be determined.) The helicopter will also not respond to its damage so there wouldn't be an issue of a particular base being able to solo helicopter by spamming sams.
The natural deterrent from spamming them would be electricity and the cost of rockets. All of this is subject to change and adjustments will be made as needed. The reason for this is to give SAMs a purpose, as well as its ammunition.