If God is to destroy every man made thing with fire on the last day,then what about shipwrecks?

The fire will be so great that the heat will evaporate all water from the earth including the oceans and destroy all things buried in it.

Evaporate the water first, than burn the ship that are wreaked

If you said "submarine" three hundred years ago. Everyone would think that you are crazy. But now we have the education to understand that term. In the future there will be something that gets the ships off of the sea floor. It will be a man-made device that allows man-kind to reach the lowest depths, and retrieve those shipwrecks. They will be back on land when God destroys the Earth with fire.

If the whole Bible is the literal truth from God Himself, then apocalyptics have a big problem on their hands: Ecclesiastes 1, 9: "What has been will be again, what has been done will be done again; there is nothing new under the sun." How exactly does that fit in to Apocalyptic, or even messianic times?

The Earth will likely die when the sun reaches its red giant phase. This will be in many millions of years, so don't sweat it. The Bible is a work of fiction and is not a reliable source of information regarding the past, present, or future.

end of the world is when Jesus kills jigsaw.

Regardless of religion, with enough heat water should evaporate and those ships should burn. You didn't think this one through very well.

The fire will be all consuming (so it even burns water)

Underwater volcanic erruptions