As many comments said, there are ways of analyzing $\mathbb{Q}^n $ as a vector space. However, they do not form a "coordinate system" for Euclidean space as we normally think about it. You can make a coordinate system which includes only rational points, but just like you said, it will be missing irrational points. It will also have odd problems, such as not forming a metric space. For instance, if you have a right triangle with legs of length 1, its hypotenuse will in fact not have a length, since it should have length $\sqrt 2$ (an irrational number) by the Pythagorean Theorem. Thus, not every pair of points has a distance between them which can be described by a rational number. Similarly, a circle of radius one would not have a rational circumference. In fact, you can't create a circle with a rational circumference in a rational only system, since those have a radii which are irrational. Also, the fact that irrational points are missing actually means MOST points are missing. This is a bit more advanced, but since the reals are an uncountable set while the rationals are countable (you can easily look up what this means and see proofs of this fact, pick your favorite). That means that nearly every point in space has irrational coordinates.
In the end, rational coordinates are simply not useful in most cases for the reasons I gave above and many more. You can create a rational coordinate system, but many things which form the foundation of modern math and interesting results, like all of calculus, would be impossible.