IMO, because the writers generally focus on advancing the action rather than characterization and development, we wind up with situations like those you describe. What always gets me is that it would be so incredibly easy to convey a lot of these layers if they made the effort. A line or two of dialogue and a facial expression would do it. Lana could ask Clark: "What were you two talking about?" or remark: "You and Chloe are always going off together to talk." or show her looking after him or over at them enviously.

A line or two of dialogue would take care of many of the vague areas and problems on the show. I don't know why they don't take the trouble to do this.