The uninstall process keeps those files, and others, around as they are considered personal data. Similar to uninstalling Office and keep .xls, .doc, etc.

As to their location, over the years Notes clients have defaulted to various install locations. Any of which can be overridden by the installer during installation.

The ususal suspects for file locations are:
c:\lotus\notes\data
c:\program files\lotus\notes\data
c:\program files\ibm\lotus\notes\data
c:\documents and settings\<username>\local settings\application data\lotus\notes\data

If you are sure you do not need to keep the users id file, personal address book, any local replicas of databases, you can delete the lotus\notes\data folder and all sub-folders.