Just do it. As long as your bolts aren't rusted beyond repair, it is an easy and free and completely reversible mod.
I personally went both ways and prefer the boards on. Yes it gives you a free "lift", but it also exposes some pretty ugly pinch welds and rotten rusty undercarriage parts. Keep in mind, I rarely wheel the truck. In fact the only off-road use has been a few beach blasts. Never crawled across anything. Massachusetts is NOT the state to live in if you like to wheel.
Ironically, my board removal mod was initiated by some urban wheeling. I did my best JohnsD90 impression and crawled up on a snow bank in a mall parking lot. Unfortunately, it had frozen rock-hard. I ended up mangling one of my boards. Off they came.
Here's how she looked without them.
I rocked the runner for a few years without boards and then got tired of hearing people complain about having to climb up into my truck (I sell real estate). So I bent the brackets back into shape and reinstalled the boards.
Here's a similar angle with them on:
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2015 Magnetic Grey Limited with Redwood interior. 275/55r20 Michelin Defender LTX on stock wheels. Daystar 2.5/1.5 puck lift.
Gone but not forgotten: Black 2000 SR5 "Highlander", Supercharged, Black pearl emblems, Factory e-Locker.