I have relocated some fixtures in our house, and now have two 3" vent stacks in the same drainage route that leads to our septic system. I'm thinking that this may be a bad idea, . . . that it may allow freezing air to enter the route. (I should say that about twenty feet of the drainage route occurs within an unheated portion of the building.) Should I cap one of the vents?
No. If you cap one, it's no longer a vent. You need vents for the plumbing to work correctly. In some cases you might combine several vents in the attic to reduce roof penetrations, but if you already have two holes in the roof there's not much to be gained by that now (perhaps when you next re-roof, if it's practical to combine them in the attic and all the sizes are make to work.)