Pin holes happen in manufacturing. Natural pinholes will be very small, not giant nicks or large chunks missing in the disc top layer. You will hardly ever spot legit pinholes without using a small flash light held up to the disc or something. It's a bit more common then people think. Most don't notice them because so many disc have fully painted labels that cover that kind of stuff up, and back in the day not many thought to do a light check on their disc every time they got a new one.
It has been happening in manufacturing since the 80s though. Its part of what error correction in Cd-drives was designed for and you really shouldn't sweat over them unless you have like more then 10 of them on a disc or something (even then the disc will probably run fine). As a by product this is why you will have disc that will work perfectly fine even though they may have thin top scratches. The error correction on compact disc is pretty solid and you kind of have to go out of you way to make a disc totally unreadable in any given section of the disc.
They were expecting it to happen in manufacturing and there is not much in the way that you can 100 percent avoid it. I have bought new sealed Saturn imports, new sealed PC games from the 90s, new music cds that are mostly unpainted, and other disc, PCE and Sega CD, that have had pinholes upon being opened. If you are the paranoid type though you can use VSO inspector to check the data sections of your disc for errors, and use EAC to error check the audio tracks to make sure your disc are fine.
As far as disc rot goes. That can cause massive discoloration and flaking off of the data layer. It can also sadly happen without any visible signs to dvds. We have had some PS2 and Gamecube games go bad on us due to rot. Godzilla, Smash Bros, Kingdom Hearts and a couple of others have been lost to it. Disc look visibly fine, but refuse to load, and they fail data checks.