loppy

Linguistically, the difference between “he died” and “he’s dead” is called aspect. As for your specific sentences:

“I thought he died” -> There was some event that ocurred which I witnessed or which I was made aware of in someway which I thought had resulted in him dieing.

“I thought he was dead” -> My understanding was that for some time up to now he was a corpse (or in some other such state). I do not necessarily know about the time or event in which he died.

You made me realize this is actually pretty common in math, e.g. “Let x, y be real numbers” instead of “Let x and y be real numbers”. I imagine this comes from the infuence of notation like “Let x, y ∈ ℝ”.