Drilling 1/4 inch holes should not be a problem at all structurally. It's best if you can drill in towards the center of the web or middle of the side of the square tubing, as the stresses in the frame member under load tend to be lowest there.
You should not have the batteries and their wiring exposed. I think that may be forbidden by DOT standards, actually; but even if it is not, having protection from the elements and from getting shorted out by debris or dropped tools is a very excellent idea.
Some sort of a shackle or U-bolt arrangement might also work well to secure things to the frame.