Seems, that if a directory, specified in TNS_ADMIN variable or in "Tnsnames directory" field on Preferences -> Database -> Advanced screen, contains multiple files, whose names starts with "tnsnames" , i.e. matching tnsnames*.* wildcard, SQL Developer is trying to merge content of all such files while constructing TNS entries used for database connections. This leads to unpredictable behavior, because sometimes duplicate entries are present, and entries not from tnsnames.ora itself are used. Is this a known feature or a bug?
It's a known feature.
Apparently SQL*Plus will do the same thing - it's just not as apparent since you don't see a connection drop down there.