Your right it slows down the PC a ton, the DB is going to shrink, and v4 will have a new DB format, that will fix this design flaw and shrink the DB even more.
I hope so, this is the only problem I have with CIS at the moment (apart from how I think BOClean integrated should have its own options in the program...)
But currently this update problem is ridiculous. I really hope that this problem will be solved because I really like CIS and want to use it but currently I can't!!