One principle from mathematics is that you cannot say that two infinities are equal to one another. For example, while there are an infinite number of natural and real numbers, these two infinities are not the same. Here you can find a derivation of the Henderson–Hasselbalch equation. Since the Henderson–Hasselbalch equation bundles up the math in a way that is difficult to analyze, lets look at the original equilibrium equation, which you can derive from the Henderson–Hasselbalch equation simply by undoing all of the steps:
$$k_a=\frac{[H^+][A^-]}{[HA]}$$
Since a strong acid dissociates completely, $k_a$ must be equal to $\frac{1}{0}$. In other words, the concentration of HA must be zero at equilibrium. Since we are doing no nuclear reactions here, this rule that my friends like to call "conservation of stuff" takes effect. In other-words, all of the strong acid that you started with must have gone somewhere (hint: it dissociated into $\ce{H+}$ and $\ce{A-}$). Now, to calculate the final pH of a strong acid solution, we use the number of protons that dissociated to find the concentration of $\ce{H+}$ and from there, the actual pH.