I have several documents with multiple layers, and by multiple I mean up to 100 or so. They are all very simple layers, most times with one word. The files are for printing to a laser engraver which has a standard shape on one layer, and the rest of the layers are single words that are centered to the shape layer. When I print, the shape layer is "visible" but not printable or selectable. Just one text layer is visible, printable, and selectable (for the purposes of printing "center/center" to the center of the wood piece being engraved). So, I'm only printing one layer at a time.
Here's the issue: The object manager obviously has a multitude of layers, all of them invisible except for the layer to be actually printed, and the shape layer visible just for visual reference. Many times, when I change a layer to invisible from visible (or vice versa), or change a layer from printable to non-printable (or vice versa), or make a layer selectable to non-selectable (or vice versa), the object manager will jump to another layer entirely, marking that layer with the change I made to the original layer (while also making the desired change to the original layer). So, it's doing its job, and then some. If I change layer 27 to "visible", for example, object manager will also jump to layer 54 and make the same change. I have to change layer 54 back to "invisible" and scroll back to layer 27 to resume work. I'm lucky, I guess, that at least it goes right to the unintended layer when it does this jumping around, but I still have to find my original layer to resume work. It happens with every change, so I'm spending a lot of time jumping all over the layer list in object manager. I can't seem to come up with a pattern for this behaviour, it seems the layers with the unintended changes are randomly chosen.
Sorry about the length of this question, but it's a little difficult to explain. I guess this might open up the discussion of "how many layers is too many layers", but these layers have extremely limited simple content.
I didn't know much about the details of the content you work with. Your current approach using layers may already be the best way to handle it. It really allows you, when you wish, to have a "small world" of specific objects for easier editing.
Having hidden layers print doesn't strike me as weird; perhaps I'm just used to it. What I find non-intuitive is that individually hidden objects don't print! I would expect hidden-by-layer and hidden-by-object to behave similarly with respect to printing.