A clear cup will show you the water level but not the level of the cut relative to the water level. So now you're back to a ruler and that's too much work for me.
I use a clear cup inside an opaque one. Roots don't like light so a clear cup would seem counterproductive there, but I do want to see when the roots branch out.
I pull the inner cup and stick it in a larger tub of some sort, water it until it overflows the hole and then let it sit for a few minutes to drain a bit (or even tilt it to drain the excess), then slide it back in the outer opaque cup and move on with my life.
Pretty easy, and that would also protect your wooden desk.