I think it is the juice/blood? of the crabs that goes black in the freezer.

I used to freeze whole crabs but they took up a lot of space (and tended to go black after a few weeks). Then I started cutting all the legs and shaking out the "water" inside - they were easier to pack together (less air in the container) and they kept better.

Now, because I bait up without using the legs or any of the shell, after I catch crabs I remove the legs, shell, lungs and guts so I am left with just the meaty bit which I cut in two lengthwise if big enough. I flick all the "water" off (sometimes use a paper towel) and pack them tightly in icecream containers. These WONT go black even after months. But ice will form in the container indicating freezer burn.

I have even gone to the trouble of freezing the meaty bits individually on trays then sprayed them with water and refreezing to put a protective layer of ice over the top. This did help a bit more - but its a bit obsessive.

Having live crabs on the beach for bait is best. I have proved that to my own satisfaction by fishing next to others. Like most frozen bait some of the "flavor" is lost. But I reckon there is another reason. If you regularly extract meat to eat by squeezing it out using a rollingpin or a bottle you know its only possible by leaving it until the crabs have been dead a day - then its easy. And easier for the lemon leaving less time for it to find my hook. Probably easing for the lice to strip the bait too.