The Wikipedia page about graphene's [electronic properties] has a different expression for the energy bands:
$$
E_1(k) = \pm\,\gamma_0\, \sqrt{1+4\cos^2\frac{ak_x}{2}
+4\cos\frac{ak_x}{2}\,\cos\frac{\sqrt{3}\ ak_y}{2}} \tag{1}
$$
which actually does give $E(k) = \pm 0$ for $k=({\large\frac{4\pi}{3a}},0)$. If we plot the square root part of the Wikipedia result we get this: (with the green sticks marking the zeroes)
And if we plot your result
$$
E_2(k) = \pm\,t\, \sqrt{3+2\cos\,\sqrt{3}\ ak_y
+4\cos\frac{3ak_x}{2}\,\cos\frac{\sqrt{3}\ ak_y}{2}} \tag{2}
$$
which is apparently also the result from [RevModPhys.81.109] we get the following (for $t=1$), where we see 10 instead of 6 zeroes and the hexagonal pattern is smaller and $30^{\large \circ}$ rotated:
There seems to be a different choice of basis (and scale). You can convert $(1)$ into $(2)$ by using: (if we assume $t=\gamma_0$)
$$
E_2(k_x,k_y) = E_1(\pm\sqrt3\, k_y, \pm\sqrt3\, k_x)
$$
and of course the degeneracy in $E_2$ is now at $(k_x,k_y)=(0,{\large \frac{4\pi}{3\sqrt3 \,a}})$