I used to have a 316SS shaft electrically insulated from the engine
through a flexible coupling and it built up calcium as you describe.
One day I threw away the flex coupling that was just helping with shaft vibration, made a new shaft out of 2205 stainless that is now electrically connected to the rest of the engine and... I haven't seen calcium deposits since. Go figure!
It is quite common, the answer is rotating the shaft periodically, even by hand, to scrape the deposits gently before they get too thick and too hard.
There have been many cutless bearings destroyed on boats that had been sitting around. I really like turning the shaft by hand to feel what is going on if the engine hasn't run for a while, it is a lot easier than replacing the cutless bearing. Once you start chewing into it, deposits form all around the shaft instead of in the grooves only and that is usually the end of it.