Let $a,b,c$ the sides of a pythagorean triangle with correlative angles $\alpha$ and $\beta$ ($\gamma$ is always $\frac{\pi}{2}$). It is known, by trascendental number theory, that $\sin\space x$ and $\cos\space x$ are transcendental when $x\ne 0$ is algebraic. Consequently $\alpha$ and $\beta$ are necessarily transcendental because $\sin\space \alpha=\frac{a}{c}$ and $\sin\space \beta=\frac{b}{c}$.
Besides $\alpha + \beta= \frac{\pi}{2}$ but this do not mean necessarily that $\alpha$ and $\beta$ are rational fractions of $\pi$.
Your question is interesting. I think the most probably, with exception of $(\alpha, \beta)$=$(\frac {\pi}{3},\frac{\pi}{6})$ is that$(\alpha, \beta)$= $(\frac{\pi}{2}-h,\frac {\pi}{2}+h)$ for some "disturbed" $h$.
I'll try to get a better answer.
NOTE.-The triangle with angles 90, 60 and 30 degrees is not Pythagorean. There are consequently no exception for pythagorean triangles. And there is just one exception for rectangle triangles according to the Niven's Theorem cited in other answer here by @Lucian.