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One thing I am cogitating about is the relationship between the size of the calibre database and memory. Calibre reads the spreadsheet data from the DB into memory so that searches and sorts can work reasonably well. If the size of that data is larger than main memory, the computer will likely start to use virtual memory, in which case performance can drop by orders of magnitude. The performance slowdown could begin with a single book, and would get rapidly worse as more books were added.
As a rough guide, compare the size of metadata.db to the amount of RAM on your computer. Free RAM after boot would be better, if you can easily get that number. Please post this info if calibre on your machine seems to have slowed down dramatically at some point.
I am not sure what, if anything, we can do with this information, but knowledge is power.
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