The largest warships lost to weather during the war were destroyers - I wrote about those losses here. Some larger ships of the period were heavily damaged by weather, but none were lost. In 1935, the Japanese Fourth Fleet ran into a typhoon. Three heavy cruisers suffered serious structural damage, as their lightly built structures buckled and flooded under the stress. Two carriers were also damaged, with both suffering damage to their bridges and flight decks, along with flooding. Nine years later, in December 1944, the USN's Task Force 38 would also encounter a typhoon. Three destroyers would capsize and sink, but larger ships would also sustain damage. Carriers were worst affected, as planes in their hangars broke lose and rolled around. Fires started aboard two carriers, with that aboard USS Monterey being very serious, and nearly causing the loss of the ship.

I'm not aware of any large warships being lost through running aground during the war. EDIT: I'm an idiot who didn't check thoroughly. The British lost the heavy cruiser Effingham in May 1940 during the Norwegian campaign, after she ran aground on Faksen Shoal in the Vestfjord. She was carrying troops and equipment to Bodo, and travelling at 23 knots to protect against air attacks. Her navigator should have been aware of the obstacle, but his plot of the ship's passage obscured the position of the rock. Nobody died in the accident, but some equipment was lost. Once everyone had been evacuated, the wreck was torpedoed by the destroyer Matabele. Beyond this, destroyers were the largest warships lost to this, with the USS Worden grounding in 1942 during the occupation of Amchitka. The USS Truxtun ran aground in a storm on the coast of Newfoundland in February 1942, along with the cargo ship Pollux. In 1940, the British destroyer HMS Sturdy ran aground in fog on Tiree Island in Scotland. That said, it was not uncommon for damaged ships to be run aground deliberately, to prevent them from sinking. During the Pearl Harbor attack, the USS Nevada was run aground deliberately to avoid her sinking in the harbour channel. The Germans grounded the cruiser Emden in April 1945 following damage by British bombing.

That said, large ships were often lost through accidents and negligence. Accidental explosions were less common than in WWI, but still occurred. In June 1943, the magazines of the Japanese battleship Mutsu exploded, destroying the ship. This was likely caused by a fire in or adjacent to the magazine which ignited unstable propellant. The British lost the American-built escort carrier Dasher to an explosion of her aviation fuel. American ships had less stringent safety standards for fuel safety than British ones, and this discrepancy led to the explosion. The RN also lost the cruiser Curacoa in an accidental collision with the liner RMS Queen Mary.