Does undef value on an entry in %INC have any useful meaning?

See require. An undef value for an entry in %INC may record the fact that an attempt to include a file failed, at least in some cases. But if it was set by means other than require, it may indicate something else. The only aspect of the value that is well defined is that it should be true if the file was included successfully and false otherwise. undef is just one of the false values.