the chances of this happening under the slab by a lightning strike seems very low, especially if it did not do any other damage.
my guess is just normal corrosion of which there are various types.
that is why many water systems are now run in plastic.
Unprotected copper pipe in concrete is subject to heavy corrosion from the outside and depending on the chemicals in the heating fluid corrosion from the inside too. The worst inside to outside corrosion will be in bends or transitions. And if a pinhole leak starts, the action of the soaked concrete surrounding it can accelerate the corrosion at that hole, enlarging it quickly.
If there is a long term low potential difference between the piping and the ground potential of the slab, it will accelerate the corrosion. If you measure a significant AC or DC voltage between the ground electrode network and the pipe before bonding, then bonding could well cause heavy corrosion, and the cause of the ground voltage offset needs to be identified before the bond is made.
So the plumber may have something behind his statement, just leave the lightning out of it.