Nate has had his suspicions about Wes' death from the beginning on How to Get Away with Murder, but it always seemed like he might know more than he was letting on. Despite the fact that the corner ruled Wes' death a result of the fire that consumed Annalise's house, Nate was convinced that Wes had died before the fire broke out. He was the only one who knew key details about the night Wes died, and "Go Cry Somewhere Else" revealed that Nate's involvement went even deeper. So did Nate kill Wes on How to Get Away with Murder?
When the explosives ignited at Annalise's house, Wes, Laurel, and Nate were inside, making them the only people who could provide any answers about that night. Wes died and Laurel didn't see much, which left Nate as the unknown in the equation. It was obvious that Nate knew something about what had gone down the night of the fire, but the extent of that knowledge wasn't clear. However, he seemed totally certain that Wes had died before being caught in the flames and "Go Cry Somewhere Else" shined a light on why: Nate saw Wes in the house while he was still alive. It's not difficult to put two and two together after that. Nate could have been so certain about the timing of Wes' death because he was the one who killed Wes.
Nate's suspicious behavior didn't end there, either; when Wes' body disappeared from the morgue, Nate acted as flummoxed as everyone else until a document was produced that made it clear Nate himself had signed off on moving Wes' body. Nate must be expert at playing dumb considering he was likely the last person to see Wes alive (barring future developments in upcoming episodes) and he kept it to himself this entire time.
For Nate to have such inside information on Wes' death, he would either have to have been responsible or have witnessed exactly what happened. If someone else killed Wes and Nate just happened to see it, then why wouldn't he speak up? What would Nate have to hide if he was innocent? However, if he killed Wes then he definitely had a good reason to keep quiet.
That brings up the question of motive. Nate could have been trying to protect Annalise, especially if he knew that Wes was planning to tell the police everything about her involvement in the other cases. Maybe Nate decided to take action by taking Wes out before that could happen.
Despite his cheating tendencies, Nate had never seemed like a truly bad guy, which made him an unexpected suspect when it came to Wes' death. But then again, it's always the ones you least expect.