It is very difficult to prove a negative. With that said, there are strong reasons to believe that the answer is no.
First, as a longtime gamer, I can say that I have ready a lot of rule books for a lot of games both independent and professionally published, and I have never seen any die roll with more than 100 sides mentioned.
I certainly do not claim to have done anything close to reading all of them of course, but I think I can claim a large enough survey that the fact I have not seen it mentioned at least suggests that if it happens it is a rare niche.
More conceptually, something like that is simply unlikely as a practical matter. Most games assume that you will be physically rolling dice and it is difficult to get ahold of dice with more than 100 sides and even 100 sided dice are rare in practice. (I have one and I still almost always use 2 d10s to simulate because the d100 is hard to read).
As mentioned in the question, d100s are often simulated by 2d10s. That is relatively simple to do and very natural for most people because we are accustomed to a base 10 number system. While there are certainly ways to simulate a fair die with a larger size than that, they all get more awkward and feel less natural. (Going to a d1000 would be easy, but you rarely need a range that large, and going for anything between 100 and 1000 would seem awkward to someone accustomed to base 10).
I should caveat though that I am excluding cases where a number of dice are rolled and simply summed together. That gives you a broader range, and is actually used in a lot of games. Several games us that as part of damage calculations and an early Star Wars RPG used it as the basis for their skill checks. But that often excludes the lower numbers so isn't simulating use of a larger die in a meaningful way and I have never seen that system described in the rules as being in place of some larger die set.