The render hit for a background rotoscope is probably negligible.
What Rob said.
Where the render hit will be felt more when/if you decide to change either the background or foreground/character elements. This is where rendering in layers and using alpha channels really pays off. If they are all to be rendered at the same time they will have to all be rerendered as well. Separating the elements out gives you options.
There are too many options to consider without knowing more about your project.
If you just want to experiment though it can be a great fun.
Render your characters without any background/ground plane. (i.e. with Alpha Channel)
Bring your characters/background into A:M as rotoscopes or layers.
Add new 3D elements as necessary. (Optional and usually not needed if you've planned well)
Adjust and rerender to taste.
The time savings is in compositing and rerendering in this case.
The hit is in setup and initial rendering.
An added plus of course that you should not overlook is that you can often use these separate elements for other things in other projects. Put your character in an ad for instance. Set up a scene a little differently for a still from the short. There are lots of possibilities.
You mention a logo for your mother's business. That is a perfect example.
Render your logo without background and you'll be able to use it in many different ways.
Alpha Channels... get to know them.