@AlifIrhas @Wolfwhistler Realistically, I think it was an executive choice by the mangaka between 'do you want to make the way mana scanners work mildly confusing and sorta convoluted but logically sound' and 'do you want to make it simple but have it be confusing in a completely different way' and for some reason, he chose the latter choice. Considering the way the scanners work, they should essentially be counters that reset once they hit a certain limit, but that would probably require some explanation, and this manga, like many before it, skimps out on stuff.
In-universe, I feel like the reason Haruto doesn't think he's above the hundreds is because of logical guesses. He has two choices, either the goddess made him so comically OP that it breaks all senses of nature, or she gave him an incredible but still stoppable cheat skill. He can't make a four-digit scanner to test either of those theories, so he just goes with the latter because it's the most logical option. The zeroes might seem like evidence to the first argument, but then you need to remember that any cheat skill that allows you to make use of much more magic then you have could probably mess with the scanners as well, and there isn't currently a safe way to test either theory, so Haruto just goes with the most logical one to him, and moves on.
The people around him all probably have varying theories on it, but basically anyone who's seen his level also knows somethings up in general and keeps it to themselves, so