Never seen any deflection issues from storing them horizontally. Most of my rods are on the heavier side of the scale but even the light rods have no issues. And they hang down there for 5+ months a years.
As far as the storing Plano trays... The area under the bait prep sink holds 4. I use that space for the trays that I need access to most often, hooks, swivels, rigging needles and crimps etc. Then I have 8 more under the port helm seat. There, everything is sorted based on type of fishing I'm doing or the species I'm targeting, ie top water, jigging, trolling, etc. I pull out whichever one I need when I need it. Bow section of my V-berth storage holds all my soft plastics in mesh lure bags. That's where I think all the Rabbit action is going on! I've got a ton of Slug-Goes and squid that I don't remember Buying!!!