Wouldn't surprise me if he had tucked the shoestrings into hisshirtpocket.
Shorts pocket. Shorts pocket! Brain fart there.
If they were just in the pocket, they could easily fall out and be found separately.
I know some kids wear their shoes without laces (don't get me started on idiotic fashion statements) but at least in the airport photo, Dylan appeared to wear his laced.
I also think that something hinkey with the laces could easily lead LE to conclude homicide.
It seems unlikely to me that there would be significant evidence on a femur (who would strike someone in the upper leg? It's also the last place you'd try to dismember someone) or phalange (seems like a long shot that anything would show up on the one finger bone that happened to be found). The clavicle/scapula would be a better possibility, but again a bit of a long shot.
So, I suspect the laces are the source of LE's certainty that the case is a homicide, possibly because they are knotted.