Why is it that in spite of the fact that the ark carried Torah tablets and other sacred objects, it was lost? Was it not taken care of by the priests of that time? Or was it destined to be lost? Why? And if the Ark is found then how will we know and verify that it is the "Ark of the Covenant"?
There is much discussion on this point among "bible scholars". They surmise it to be anywhere from Yemen to Ethiopia among other far flung locales. I believe the Gemara in Megilla on 26a must be read to mean that the Ark is somewhere on the Temple Mount (in the catacombs beneath it).
It is a little complicated to explain. If you're interested drop me a line at email@example.com and I will go into a lengthy explanation.
The suffering question is a complicated one best addressed separately.
As for the Ark: it was cared-for quite well (well it was briefly seized by the Philistines ~3000 years ago but soon after returned). The traditional Jewish view has it that about 2500 years ago, they knew the Babylonians were going to plunder the First Temple. To keep the Ark out of the Babylonians' hands, the king buried it somewhere beneath Jerusalem -- where it has most likely been ever since.