Should I cap one vent in a two vent stack?
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.)