The water pump or the rad could be bad which caused the overheating issue, but the water pump would not have had anything to do with a thud upon trying too start the engine. The water pump impellar doesn't have anything it can hit, and if it did it is unlikely you would here it. Even if it froze, it is belt driven an d you should have heard the belt sqeel on teh stuck water pump pulley. I imagine if the t-belt broke it could have caused a thud, but if it was a loud thud, I would agree with OOP's that you probably hydro-locked it.

More than tread lightly. Leave it like you were never there, nor anyone else.
'90 X-cab 4.88's 33 BFG AT's, rr ARB, Headers, Ignition upgrade, cold air induction.
'91 X-cab 5.29's 315's BFG MT's, rr ARB, custom bumper and flatbed