You will want to keep all holes for the rod holders above the waterline. Generally speaking, placing the holders outside, rather than on the top of the deck, leads to being in the way during paddle strokes. Also the mounts tend to take more hits to rocks (river only issue) and snag on things while in transport. Both of which can lead to the screw holes widening/deforming/tearing out.
I use similar mounts (Rod Tender Twin Pack), but have mine mounted on a milk crate that is strapped down behind my kayak seat. I don't like to have any obstructions in front of me.
I highly suggest that one use their kayak several times before adding hardware to refine location.
PS I don't know about your sonar question, I never have used one on a kayak and have no plans to ever use one (on a kayak)