For information, on my computer (Ubuntu 20.04 LTS + GTK2 + Lazarus 2.0.4 + fpc 3.0.4), the Hint property of a control is visible, whether the control is placed over a TPanel container, or directly over the TForm, if its property ShowHint=True and its property ParentShowHint=False (same thing for the hints of the controls of a TDialogXyz, also placed on a TPanel).
So, I don't think it's a GTK2 problem.