Unfortunately the calibre debug log doesn't give any information about why this might be happening. A
CC debug log would tell more.
That said, my first guess is that the problem is that CC's "scan for new books" is taking a very long time. Try turning that off in Settings / Connecting to calibre / Wireless Device connection / Scan on connect. Another possibility is that the file system performance has tanked because of the number of books. See our FAQ
[Android] I have added a lot of books and now adding books takes forever. What do I do? for more information. A third possibility is that CC is running out of memory.
If none of the above helps then send me a CC debug log. As I said above, that should tell me what CC thinks it is doing.