So to keep things simple lets say I beam some x-rays at the crystal at a 90 degree angle of incidence so we can ignore the sinθ part of the equation.
You can't think it like that: if you place the incident beam perpendicular to a given plane, then different planes are not perpendicular anymore.
When you shine an X-ray beam onto a crystal, light is diffracted in specific directions that are governed by Braggs law. You measure the angles of all the reflections. At that point you know λ, you've measured θ, so you can determine distances between planes. And because the intensity of diffracted light is proportional to the number of electrons each atom has, you can mathematically work out a crystal structure.
That's the general principal. In reality crystals are never perfect and we can't measure the diffracted light phase, making solving crystal structures very tricky.