Gory detail:
There are two catalogs (or more!), a system catalog and then one for each path you've created a database on.
db2 LIST DATABASE DIRECTORY
-> System catalog
db2 LIST DATABASE DIRECTORY ON /my/path/where/databases/are
-> Physical database catalog
You can only connect/drop/etc. if they are in the System catalog.
In general, you DON'T want to delete the NODE0000 directory... you can always get around this by re-cataloging and dropping like sathyaram_s suggests!