If you don't want the roof rails don't bother with them. I suspect they were there more for show than anything else, since you have a lot of things on the roof that would make ratchet-strapping things to those roof rails difficult. They certainly won't have been added to give any extra structural rigidity to the roof.
I would want the top of that ladder screwed down, but that would mean screwing it through your roof membrane and every time you do that you introduce more options for leaks. That is magnified if you use the ladder since each time you pull on it you will be putting strain on the screws and any sealant there. One of the leaks I had in the rear of my Shadow Cruiser was due to an awning that was attached to a rail screwed to the back wall. The weight of the awning bouncing up and down resulted in a gap around one of the screws securing the rail allowing water to penetrate.
Steve.