For a moment I would like to keep Quantum science apart and just dive into Mathematics. It grants us to measure a side with integral length to infinite accuracy (i.e. if a line is of $2$ units then it can be said with full certainty that it has $2.000...$).
Given a right triangle with $base = 1$ unit and $height = 1$ unit, Maths allows us to measure the side with infinite accuracy but just when we join those two lines to get a hypotenuse then we are left with an irrational number $\sqrt2$ about which we are certain that we won't ever be certain (about its length).
My question is, what is the difference between two perpendicular lines and a line which is inclined? What makes it so different than a base (or height) such that it is unmeasurable ?
(This was originally a comment, but posted as an answer, as per request from OP)
You say you don't want to involve QM (by which I suppose you mean any physical situation where you would actually have to measure something), but your idea of "measuring" something seems very "physical". If Pythagoras tells you that the hypotenuse is $\sqrt{2}$ long, then you do know it to infinite precision. I could also say that if you were measuring the lengths with a ruler, how would you know that $1.000\dots$ actually continued to be zeros all the way? As a third option, just define the hypotenuse as the unit for your ruler... then the other two sides are irrational.