Preserving organic materials or organisms in salt requires more than just laying on top of a salty layer.
It requires complete coverage with salt and frequent renewal of the salt, to remove the salt saturated with the water extracted from the organism.
Considering that your Kraken, whatever it is made of, is 50 meters long, I think only a very minor part of its body would be in contact with salt.
Decomposition of the body would then be unavoidable.
If you want to preserve the bodies in salt, they should have parts with low water content (if you dehydrate a jellyfish you will end up with nothing). A Kraken, being often depicted as a sort of cephalopod, has practically no hard parts.
If you handwave this and somehow manage to properly prepare the body in salt (and I assume a magical organization capable of emptying a bay can also manage to stir some Krakens in salt) by completely covering it in salt, your best bet is to cover the whole volume with non permeable materials, like clay. If layers of clay preserved rock salt in the bottom of the sea, they can presumably protect your salted Krakens for a couple of millenia.