At around the 12,000 books you'll notice it does take a bit longer to start up. And a little longer to finish searches or select an individual tag.

My solution was to have multiple libraries and separate your books by subject. One library for science fiction, one for technical textbooks, one for historical, one for other non-fiction... It's fairly quick and easy to switch between libraries, so this way each one doesn't get too large.

I use the same library files on a hard drive with a linux and a windows Calibre. There's really no difference there just based on OS.

Just a side thought here. Those zipped up files containing all the daily IRC book submissions I suspect you're working with actually contain an awful lot of garbage. There's many subjects you're just not going to care for, no matter how varied your reading style is. They also contain a LOT of multiple copies of the same book in many formats you'll never need. And the same book will be in there, up to several hundred times, with just slight variations in the file name. So, you're importing about 80% of those files for nothing.

You may want to actually look through the files on your hard drive before you bother with putting them into Calibre. Concentrate on the ones you actually want to have and preserve. Then start cleaning those up with metadata and good cover images. Trust me, in this case, quantity is just really not a good thing.