It looks like I bumped into this as well, although I didn't dig into the code because we found a work around.
The documentation seems to indicate that the schema allows 2 types of java-hints: 1) global hints, and 2) classification hints. What I mean by (1) is the java-hint tag is not nested, and (2) means it is nested under windup:classification. The (2) type does not display in the reports, and I cannot get the tool to spit out any error about the difference. Type (1) works and displays the hint in reports.
I'm going to sync down the latest source to see if there was a fix...
The current underlaying code does not support classification hints.
I am currently working on getting that working.
Upon further investigation it appears java-hints with source-type="IMPORT" do not print the hint but
those with source-type="METHOD" do.