Patents only offer you protection against detectable infringement. If it's possible for company A to keep their algorithm secret, it's possible for company B to keep their infringement secret.

I understand that, but in the examples given in this thread of CS areas that are lacking published research, it is pretty clear that companies develop technologies in secret because secrecy provides them with more value and serves as a better protection against competitors than patents would. You just can't make a financial firm share their trading recipes that have any sort of value. We're lucky they don't patent trading/financial versions of 1-click-to-buy.