Considering that Shia LaBeouf hasn’t expressed any interest in returning to the Transformers series, the only way we’ll know for sure what’s happened to Sam Witwicky is if Transformers 6 or a later movie directly mentions him.
Just because his last name is Witwicky doesn’t necessarily means Sam has been directly affiliated with the organization following Dark of the Moon.
Still, at least now we know his connection to the Transformers extends beyond what was shown on screen years back.
However, if he was fulfilling his Witwiccan duties, then that means he is indeed dead, though that still doesn’t explain when he died and how.