Boat decks, unlike a house are not generally set up to span long distances without support.
If you need to remove the pillars to get the tanks out thats one thing. Leaving them out for the long term is hard to say from the backside of a keyboard but in my opinion probably not the best idea.
As far as plywood attached to them, well in my opinion you cannot get too much wall space in a engine room. Every inch of vertical space in an engine room is a inch that can potentially get something screwed to it in the future. I would want every bit of vertical walls I could get for future equipment mounting.
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