For any serious trail riding, the brakes and 10-speed shifter are definitely worth it. There's no question its worth the money from that perspective.

Having said that, get the cheaper bike with the better paint. The differences in components will only show up when you start pushing the bike to its limits. A hybrid is an inherently compromised design, its best for cruising around town. You will rarely be shifting aggressively, and even low end Shimano hydraulics are excellent compared to hydraulics from a few years ago. They'll get the job done, reliably and without complaint. Shifters are the same way. They may not shift downshift flawlessly when climbing a 12+% grade, but chances are, you'll never be doing that.