Sketching on paper vs. working in 3D is a long-debated topic in architecture as well as level design. I think it is a very valuable skill to be able to not necessarily design in 2D, but to be able to communicate the
idea of a layout through 2D sketches. That is to say, the sketch is a jumping off point, a way to work through some bigger picture design problems, and the layout can later be refined and evaluated in 3D software.
Typically just a plan sketch is not enough - you may need multiple plans or section cuts / elevations to communicate height variation. You might also choose to learn how to sketch in 3D, although this can become complicated quickly.
I bring this up because I think being able to communicate a 3D design through 2D means is a cornerstone of the architectural discipline, and it is a valuable skill to have. It's less important with level design, since your 3D software builds the final result, rather than in architecture, where your 3D model exists to produce construction drawings. Regardless, the ability to sketch builds some useful skills:
1) Ability to communicate a 3D environment through 2D means (which even includes things like how to take good screenshots)
2) Ability to understand plan drawings more completely
3) Ability to work through design problems and take notes when you aren't at your computer
tl;dr: I agree that beginners who design on paper are less likely to understand how to utilize height variation, and you should be doing the majority of your design work in the editor. I just want to also advocate for sketching as a useful tool to have at your disposal.