If someone owns stock in a company that will benefit greatly from these tariff refunds, and the stock price goes up on Shabbat because of the news, does this violate any prohibition of benefiting from work done on Shabbat?

No, owning investments that appreciate on Shabbat is permissible. You can hold assets through Shabbat as value changes occur without your active involvement. The prohibition is against actively working, trading, buying, selling, or even discussing investments on Shabbat. Passive appreciation/depreciation is not considered work. So, hold your investments, but do not actively trade or discuss them on Shabbat.