BUG: Adding highlight enables disabled notebook

I think what you are saying is that adding a note / highlight to a Notebook automatically enables that Notebook in the resource.

This has been true for a long time - see https://community.logos.com/forums/p/96841/667534.aspx#667534 for mention of it under the old Notes system - and I think it is the right behaviour.

Otherwise there would be a lot of support calls saying that highlights weren't appearing.

Am I misunderstanding what you are describing?

If many resources have Notebooks enabled, response time slows to a crawl.

I'm not commenting on this but something to explore if I am understanding your initial point properly.

that highlights are now treated the same as Notes. They did not appear in Notes documents.

Highlights have appeared in Notes Documents for a long time - depending on how they were set up they may not have appeared in the same Notes Document as the Notes you made.

And this capability is still available in Logos 8.

I'd love to know how to set this up, if you're willing to explain.

For each highlighting palette (hover over its name to get the triangular dropdown) you can specify which Notebook to use for highlights from that palette.

As per the screenshot, this can either be the Active Notebook (this is the default), No Notebook, or any named notebook of your choice

(There was something similar in Logos 7 where there was also the option to specify Palette-specific or Resource-specific Notes Documents)

Does this help at all?