The circumstances clearly suggest that Marco ran away, but in my opinion, it seems that he was the victim of a crime... the fact that he left the house barefoot tells me that he did not plan to be gone for too long, and it seems very unlikely that a child nine-year-old had the resources necessary to adopt a new identity and live undetected for 24 years...
it's also possible that Marco ran away, but was kidnapped by a child predator... he could also have seen something he wasn't supposed to see and died as a result... the part of Miami he disappeared from is a high crime area, and I imagine it wasn't much better in 1994..
and lastly, his mother killed him (possibly by accident while they were arguing) and forged the note to make it look like he had run away again... however, I personally feel uncomfortable speculating too much about his mother's guilt considering the lack of evidence... it doesn't sound like they had the best home life (there was at least one case of domestic violence and Livia was in rehab for drug addiction), but there's a big difference between hitting your husband with a bottle and killing to your own son...
It's tragic that there is almost no information about this little guy. Frankly, it doesn't seem like the authorities tried very hard to find him, and I can't help but wonder if his race and his financial situation have something to do with it... I also wonder if this would have been solved if they had tried harder ...
either way
rest in peace