Depends on what kind of probes you use. I have several. I run the cheap oven probes through them, because the lid will eventually kill them by breaking the small internal wires. I also have a couple of thermocouple probes which have a 1/8" stainless armour around them. I HAVE to run them through the holes, or bad things would happen.
But, I also have some ambient thermos with oven clips on the ends. Obviously these won't fit in the existing holes, so I take my changes running them through the lid. But I have already killed a couple this way.
I guess the short answer is, yea, you should use the existing holes. And, no, I wouldn't add any new holes. The more holes, the more leaks.
Also, after I run the probes through the holes, I stuff foil in the gaps for a better seal.
