Pre-compose, simplify, render and replace. The most efficient workflow depends entirely on what is going on in each layer.
Shape layers can start to slow things down if there are a lot of paths. Nothing is keeping you from moving sections of the shape layer to different layers. I see this kind of slowdown when people unnecessarily convert vector layers (Illustrator) to shape layers. Unless you are animating vector paths, using shape layer animators, or using the C4D rendering engine to extrude a layer, there is almost never a good reason to convert vector artwork to shape layers.
I use the Composition menu to Pre-render all the time. I've customized the settings to fit my workflow. I also never edit a movie in After Effects. My compositions are never longer than a single phrase or sentence. The only time I ever have more than one shot in a composition is when I need to do a transition between shots that cannot be done in my NLE. There are lots of ways to streamline your workflow and lots of ways to efficiently work with very complex compositions that don't slow down your system.
If you share screenshots showing the structure of your comp and describe the design goals in detail we might be able to help you work more efficiently.