Q1 Depends what you have in mind. A roofer would prefer low roof, easier to reach and to tie on his ladders whereas a gardner say, may prefer a high top so he can stand up straight whilst moving his gear in and out. If in doubt get an high top, you don't have to use it.
Q2 You only need a rear ladder if you have a roof rack, again you know best. They do use extra fuel and cause a lot of wind noise though and are dodgy when frozen or wet.
Another take I have seen on the above was a high top with a false floor about 18" high inside the van. The guys fitted industrial doors and had triple section ladders under the floor. This saved them having a roof rack,
but they knew how high they were working and this wouldn't suit everyone.
Q3 & Q4 Have a look in YP or similar for van liners etc. They stock roofracks,security gear, towbars, vanvaults, racking etc. Deal direct and avoid the dealer mark-up, they will also discuss the latest kit with you.
Security of the van itself is less of an issue these days as they won't start without the keys. Keep these out of sight at home and on site. Consider mortice locks and take the key for these off the ring when your van is in for service or repair. Your tools are the biggest issue, don't broadcast them to all and sundry, keep your doors closed from prying eyes whenever possible. Your tools are your livelyhood never leave anything unattended if at all possible. Also avoid lending gear out on sites.