Bookmarks are stored in a database, this is a file with the extension .wsw
The number of bookmarks per database is not limited, but the more bookmarks you have in a database the more resources are used. Probably WebSite-Watcher can slow down with lots of bookmarks.
We personally don't use more than approximately 10.000 bookmarks per database. But simply try to use more bookmarks on your system and see how it performs as this is dependent from various factors (CPU, RAM; 32/64 bit, etc)
The number of databases is unlimited (or only limited due to hard disk space), you can open databases with File+Open. If you have hundreds of thousands of bookmarks then you should divide them into different databases.