seraph7, you can turn off update notices in the preferences. Just keep an eye on Calibre's
changelog and only update when you think it is critical/wanted.
So far my library is at ~22.000 items, and although there is a performance hit while browsing the full library it can handle it just fine (I use the linux version btw) and when you restrict by, say, author or whatever it zooms along just fine.
...But I still wish it had a MySQL backend...