Note: Even though what I'm going to talk about below focuses on scanlines, this really applies to all CRT simulation effects such as the shadowmask effect and so on, but it's just easiest to use scanlines to illustrate what's going on.
No. You don't need the vertical variants when you rotate.
Scanlines on arcade monitors are horizontal.

That means that when you physically rotate a monitor, the scanlines should be vertical.

The problem with the GLSL shaders is that they're dumb, and if you're playing a vertical game in a landscape/horizontal orientation, it will continue to give you horizontal scanlines even though in vertical games, the scanlines should look like they're vertical.
When you use the vertical variant, it allows you to play in a horizontal monitor orientation and still get vertical scanlines. It is NOT for a vertical orientation.
Vertical scanlines:

Horizontal scanlines:

When you tell MAME to rotate your monitor, you're also rotating the scanlines, so you're already getting the proper scanlines and don't need to use the separate shader.
Basically, the bulletproof test to make sure you're getting the right results is to verify that you have vertical scanlines in vertical games and horizontal scanlines in horizontal games.