So The Necronomicon is a 1-handed tome that gets placed in your threat area, but does it still take up one of your hand slots? I mean it has to, otherwise the 1-hand symbol is pointless right? Any other threats that take up your slots?

It obviously does. It's one of it's downsides. If you're unlucky enough to have both of your hands full when you draw it, then you'll even have to discard one of the things you're holding.

Or put it in your tote bag!