I think you're over thinking it...
I had the lift without the warn hubs for 1 year, with no problems. Since then I have gotten the hubs, and only had one CV boot go, and that was after having the lift for 3 years. I know people who have gone w/o the hubs for a few years without CV issues... if I were you, I would wait until the issue comes up.
Besides, if you're taking it off road, you could ram a stick up into the CV boot a week after you swap it out...
As for the hubs, I typically leave the hubs locked for weeks at a time in the winter... if there is a chance that there will be snow, I lock them, then I am ready to go. I typically forget to unlock them right away... so they stay locked for a while. You could by rights leave them locked all winter, and do no harm... it would be like leaving the truck stock. That said, you'd only see the benefits of the manual hubs in the remaining months of the year.