They were binned at the factory. If a certain SMM was determined faulty or it potentially couldn't keep up with the rest, it was deactivated. 980 Ti has two disabled, so whether two were bad or not can't be known to the end user. Maybe one was, maybe both were. Either way they were disabled and the rest were considered good else the chip would've been labeled as totally defective.
This has been going on for a very long time and I can't think of one issue where someone has had "other issues" with the chip that weren't found at the factory. The manufacturers have a good idea of what the potential problem spots are long before binned chips make their way to the consumer.
The reason the rest can clock so well is that slow or faulty transistors usually congregate in an area of a die. If they disable that area, the rest should be really good and can clock quite well. Without the slow ones holding them back, it can be a screamer.
It's also not totally uncommon for perfectly good chips to have sections disabled. Maybe certain areas simply didn't clock as high, or they were a bit worse at power leakage.
Back in the olden days I had an Nvidia 6800 which was a 6800GT with a few pipes shut down by the BIOS. Now, these pipes could've been bad or, in the case of certain AIB partners, it made more sense to slash a working chip and sell for lower margins but higher volumes. I unlocked my four remaining pipes on my 6800 turning it into a 6800GT with a BIOS flash. That card still works to this day in an Ubuntu machine for general internet, music, and word processing. Occasional but very limited 3D games still work fine on it, besides the fact that it's old as snot.
Edit: It's too bad this can't be done today. Nowadays they actually slice the offending sections with a laser.
