Bugs that could corrupt your data are highly unlikely. The part that deals with data is mostly written in python and that code is common to both 32 and 64 bit installs, it doesn't care about 32 vs. 64 bit. That same code has been running in 64 bit linux and osx installs for many years.
However, computers are highly complex systems and there are never any guarantees. As always, you should make frequent backups of your data.
To answer your specific question, calibre does not touch ebook files unless you do a conversion, so yes only the metadata.db file and any files you convert are at risk.
On a technical note:
The bugs that I think are likely are mostly crashes caused by the fact that windows has different sizes for the long datatype (LLP64 instead of LP64) from unix systems and all the C/C++ libraries that calibre uses are all primarily developed for Unix systems. Some of those libraries probably make assumptions about pointers fitting in integer datatypes that are not true on windows.
Last edited by kovidgoyal; 12-05-2012 at 02:32 PM.