Every consistent first-order axiomatic system has models of every cardinality. Given this fact, if your modified axioms has ${\mathbb{Q}}^3$ as a model, then ${\mathbb{Q}}^3$ will not be a unique model. However it still makes sense to ask if ${\mathbb{Q}}^3$ is a unique model.
So long as your modification uses only countably many symbols, then there will always be a countable models. Countable models are "discrete" in a sense.
In Hilbert's original writings, he came up with a concrete countable model to his axiomatization of Euclidean geometry. This model is the smallest Pythaogrean field containing ${\mathbb{Q}}$, i.e. $a^2+b^2$ \sqrt{a^2+b^2}$ is in the field if $a$ and $b$ are. If you allow adding irrational points, this countable model is an instance of a discrete model.

