Choppy Playback even in small motion graphics

10,000 layer comps, even 1,000 layer comps are not really doable in After Effects. I don't know where you would have seen that. AE breaks down fairly quickly with too many comps in the timeline. You would have to shy a bunch of them to find the layers you want to work on. 

AE is not an editing app. Most comps are one shot or one animated idea. Most of the pros that use AE only use it to create a shot or animation that they cannot create in an NLE. Final films are edited in an NLE like Premiere Pro or even Davinci. 

Most of my comps are under seven seconds. Occasionally, if I can't do a transition any other way, I will make a comp that is as long as a sentence or phrase or 4 bars of music. Composites, and or animations that I work on may have a dozen or more nested comps, and each comp may have 10 or 20 layers but I would never have a thousand layers in a comp. There would be no way to keep track of that many effects, mattes, overlays, or color corrections and I can't think of a single shot in any movie I have ever seen that would need more than a hundred or so total individual elements. 

That said when working in AE, or a 3D app, or even in my NLE on two-hour-long feature films, I use the Pencil Test / Ink and paint workflow developed by animators more than 100 years ago. A pencil test is where you block out the ideas, timing, composition, framing, and action in a shot. In AE, that means 50% or less Magnification Ratio in the Comp Panel, no motion blur, minimum effects, if necessary I skip a frame and the comp panel resolution is set to auto. All I am looking for is framing, blocking (how the action works), and timing. When that is good I'll turn on or add effects, check blend modes, finalize the color in my Ink and Paint phase. I never rely on ram previews of the full shot for this part unless the comp is very simple and will quickly render. All I need to see are a few hero frames, then the shot can be rendered as a lossless DI (digital intermediate) to be sent to the NLE and/or an H.264 proof to be sent to the client, editor, or director for approval. I use a background renderer most of the time for complex comps so I can start work on the next shot and I don't like to wait for renders because I never have been paid to sit around a wait for a render. I only get paid to create.

Try playing back your animations with minimal effects and reduced resolution to check the timing. Skip frames if you need to. All you need to see is the timing and blocking. When that is done, turn everything on and finalize the look and render, then move on to the next comp.