The "black earth" is your top soil layer. Traditionally you should always scrape your top soil leyer off before you build. Whether you are builting a pole barn, or a full foundation you will need to go down below frost depth regardless with you pole/foundation. Chances are that in your location it is 48" or deeper. I agree that you should check with your local code/building dept for the regulations. If your location is anything like mine though you may not have a building dept, or any enforceable code to build by, especially with an agricultural use. I would check the min frost depth regardless though in the International Residental Code, I beleive if has locations listed in Canada, if not your closest city should have a building dept that could tell you that.
As for removing the top soil though, that is just industry standard. Depending on what you plan on doing for a floor you may be able to leave it and just remove the vegative layer. A stone floor with light use may hold up with the topsoil in place, but with heavier use, tractors, equipment ect., it may not hold up well. Just my opinion though, I do realize that 100 +/- ton of stone is more then most are willing to do.