Does After Effects actually take time “Processing” shy or hidden layers?

Once After Effects sees that a layer is hidden, it moves on to the next layer (shy or not shy).

The project will probably launch and save faster and probably render faster without the additional layers to keep track of, but I doubt that it would be significant enough to give up the convenicne of having those layers in the project should you want to make changes later.

The AE render API does a number of prefetch tests based on the actual project structure and visibility (as would anyone writing a sensible render engine). There's nothing to worry about and removing items from the project doesn't yield any further gains. This would only make sense if you have e.g. cache-dependent effects like Warp Stabilizer and/ or something is really busted and slows down overall performance like a leaky effect, a corrupted cache or a messy expression reference to one of those invisible/ unused footage items.

Mylenium