As long as you don't take out all the seats you have nothing to worry about. since you said you want to put in gun boxes, and that, that will put the strength back into it. You might want to think about leavein' the back bench in though. I've taken the seats out of 5 different boats, and have never had a problem.
Life's journey is not to arrive safely at the grave in a well preserved body, but rather to skid in sideways, totally worn out, shouting"...Holy crap...what a ride!"