I have a fundamental misunderstanding about Airy wave theory. All the texts that derive the dispersion relation for gravity water waves use as a final step the unsteady Bernoulli equation: $$\frac{\mathrm d\Phi}{\mathrm dt} + g\eta = 0 .$$ But as far as I know, the unsteady Bernoulli equation also includes a squared-velocity term (and a pressure term that is constant), so it must indeed by written as $$\frac{\mathrm d\Phi}{\mathrm dt} + \frac12(v_x^2 + v_y^2) + g\eta = 0. $$ Now comes the point: if the fluid particles move in circles in constant speed, then the term $$\frac12(v_x^2 + v_y^2) $$ is also constant (like the atmospheric pressure) so the Bernoulli equation reduces to the familiar equation.
This assumption is indeed correct in deep water, but in intermediary water depth and shallow water it's not correct, but I have seen cases in which the Airy wave theory is also applied in this regimes. So what did I miss?