Migrating input formats for taxonomies with empty description
The field is empty so it'll get a format set from the configured default when someone enters a description. If there's no value it doesn't need a format, because the format is purely there to say how the value should be displayed. 

In theory a value of an empty string with a format attached might give a different result to a null value (the empty string might be wrapped in &lt;p&gt; tags for example) but this will not usually matter in practice.

So the migration is doing what is expected, by not creating an entry for an empty field value.