I installed running boards on my third generation 4Runner. Most of it was installed underneath with nuts and bolts, no drilling required. I had to drill one 1/8" hole in the rear wheel wheel, it came with a screw type bolt and nut. I figured if I ever removed the running boards, I could re-install the nut and bolt in the hole.
I know the 4th generation may be different. My point is, Toyota has been making the 4Runner for awhile. I doubt they made it hard for someone to install or uninstall the running boards. Also, I doubt they had to make many new holes. Hopefully, if there are any holes, all you have to do is put the small bolt back in and maybe a touch of rustoleum in the back of the hole.
If you look closely, especially underneath you will problably see how it was put on. If you become the first to uninstall the running boards, you could write something up on this board for others to follow.