Because, if you do the math it'll pop out. The resulting wavefunction is mutually orthogonal to wavefunction 2 and constitutes a valid representation of E1, that came from performing the projection operator on D6h using p-orbitals as your basis set..
Now, who ever told you a node couldn't pass through atoms in the first place? Remember all of this is based on quantum mechanics and group theory, so don't assume you can make sense from it. If you continue with Chemistry, you will be able to come back to these basic ideas and fully understand what is going on.