The only harm I see in adding numbers is that it takes up more space, and in some cases may make it that the entire heading no longer fits on one line, or a heading on the left runs into a heading on the right.
I don't think it's so much a matter of weighing gain versus harm, as a "why bother". I'm hard pressed to think of cases where I say, "Now I want to flip to section 6.3". If it's something I've already read, I'm more likely to remember the title than the number. If I'm flipping through a book I haven't read before looking for material of interest to me, I might well say, "Stochastic methods, that's something I've always been curious about." I can't imagine saying, "I've always wanted to read a section numbered 6.12 -- so many book end chapter 6 with section 11."
Sure, if a book has cross references that say "see equation 5.3", then it should have chapter numbers in the page headers or footers. But even with that, if chapter 5 is long and has only a few equations, finding equation 5.3 could still be a search. A well-designed book would give the page number.
Sometimes when you ask, "Why don't people do good thing X?", the answer is, "Because they're lazy and or stupid", sometimes it's "because there is this really good reason to NOT do it", and sometimes, as here, it's "because it isn't all that great an idea, it might help sometimes, but most people don't care enough to bother."