One of the more prominent uses of sqlite in Firefox is the 'places' db where your history and bookmarks are stored. If you go to
History->Show All History, then select a few thousand entries and press delete, you can lock firefox up for several minutes, tens of minutes even.
I don't think this is necessarily damning of sqlite though, I'm pretty sure Firefox is not quite doing things right in some cases. I can delete thousands of rows in sqlite in mere milliseconds, so something else is going on. A shitty schema maybe? I'm not sure.