There are a couple common points of confusion which I would like to address.
Not all interactions are dictated by symmetries. Yes, symmetry is of course always important to physical understanding. And yes, the Standard Model is a gauge theory, and so the interactions of the fields with the gauge bosons are dictated by their representations under the gauge groups. For simplicity, just think about a 4d theory of some real scalar fields $\phi_i$, $i=1..n$. Their dynamics are governed by some Lagrangian of a general form
$$
\mathcal{L} = m_i^2 \phi_i^2 + \rho_{ijk} \phi_i \phi_j \phi_k + \lambda_{ijkl} \phi_i \phi_j \phi_k \phi_l,
$$
where I have used the freedom from the broken $O(n)$ to diagonalize the mass term (that is, to go to the mass basis). The coefficients $\rho_{ijk}$ and $\lambda_{ijkl}$ and symmetric tensors which parametrize some general interactions between these fields. The strength of these interactions are not governed by any 'quantum numbers', but are rather free parameters in this theory.
And indeed, this is just the situation with the Yukawa couplings in the Standard Model. Recall the Yukawa sector of the SM Lagrangian,
$$
\mathcal{L} = y^u_{ij} \tilde{H} Q_i \bar u_j + y^d_{ij} H Q_i \bar d_j + y^e_{ij} H L_i \bar e_j,
$$
where I prefer the convention of working with left-handed Weyl fermion fields $\lbrace Q,\bar u, \bar d, L, \bar e \rbrace$. The sizes of the Yukawa couplings $\lbrace y^u, y^d, y^e \rbrace$ are likewise not governed by any symmetry demands, but are instead free parameters of this theory which are to be fit by experiment. Indeed it is true that after the Higgs condenses and gets a vev $v$, these Yukawa interactions provide mass terms for the charged fermions $m^u_{ij} = y^u_{ij} v/\sqrt{2}$ etc. And this is how we fit the eigenvalues of the Yukawa matrices.
But to some extent that is getting ahead of ourselves as far as this question is concerned. In the unbroken phase, these couplings still have an independent life of their own! Indeed, even if we modified the theory such that electroweak symmetry were never broken, these are still real physical parameters. They control the interactions of two fermions, say $Q_i$ and $\bar u_j$ with the Higgs field $H$. For example, with these numbers as inputs into our Lagrangian we could calculate how likely it is if I collide a $Q_i$ and a $\bar u_j$, that I produce a Higgs boson. Or you can think about the early universe when there were lots of Higgses in the hot, dense plasma, and this coupling will tell you how often one of those Higgses will collide with a $Q_i$ to produce a $\bar u_j$.
Let me make a final comment about another more-elementary-particle-physics way one may like to think about this. After electroweak symmetry breaking, when the Higgs gets a vev and you go to the mass basis, the Yukawas still control the coupling of the fermions to the Higgs boson. The Higgs boson mediates a Yukawa force just like the pions do---it's just that the Higgs is much more massive, so the range of this Yukawa force is very small. So these Yukawa couplings control the size of the Yukawa force between the different fermions which is mediated by the Higgs field.
TL;DR: Before or after electroweak symmetry breaking, the different generations of SM fermions interact differently with the Higgs field, and so can be distinguished.