Either he was lying (unlikely), or Ishamael implied that he and the Dragon had fought numerous (thousands?) of times which would mean that the Dark One's 'prison' had been drilled into over and over and over again.

The Wheel weaves the Pattern, but apparently the Wheel weaves a similar Pattern each time, else why would the DO want to break the Wheel and destroy it for all time. It seems as though each time he is freed, imprisoned and freed again, over and over.

That sounds like the Creator intended it to happen, maybe to give all humans free will to choose to follow the DO, or not. Just as the Creator does not stop someone from using the One Power for good or evil. Thus Lanfear aka Mieren may have been destined to drill the bore over and over and over again, or it could have been someone else, but someone always did it.

Then again maybe Ishamael is talking about the Mirrors of the Wheel, where in alternate realities the same battles are being taken place and the whole drilling only happened once, yet across all the realities. How he would know this, I dont know. Maybe it was only conjecture on his part.

My thoughts are that Ishamael is not talking about the alternate realities and in fact is stating that in this reality he and the Dragon have fought countless times, thus the DO has always been there and was destined to have someone drill the bore every time over and over again. Even if Rand wins TG it wouldn't mean that it won't happen again and again, so likely he will only defeat, not destroy the DO forever...