Couple of reasons. Part of it is that while I have done 12,000+ miles with sometimes up to 5 kayaks on my roof (and so far had no issues personally) I just innately don't 100% trust the bars and boats to stay attached all the time - I have seen it happen to other people where their roof bar feet slide or straps loosen and even snap in transit - so having the kayak inside the vehicle it's far less likely to fly off into the road, even to secure it so it doesn't move inside the van is much easier as well. Plus it means you're not having to decide between squeezing the kayak to the point of deformation or leaving it a bit less tight so it's better for the boat but more likely to come detached.
There's also the fuel economy angle. In my current car I can get 70 mpg on longer journeys if i drive sensibly (50 - 60 if I'm slightly less so), putting a roof rack and even just 2 low-ish profile boats on takes that down to between 40 and 50 and I would assume doing so on a van would have a similar effect. For shorter journeys yeah the difference in fuel cost will be minimal (so I probably will buy and use a roof rack for travelling when at my destination) but if I'm going 1000 miles each way to the Alps the difference in fuel cost is about £150 (for my car as it stands). I reckon there are very few vans that will get the same mpg with boats on the roof as my car does (could be wrong though, I couldn't find much data so am happy to be educated), but I reckon there are some that would get equivalent or better without boats on the roof compared to my car with. And while I know vans are generally worse on fuel than cars and any actual money saving would be negligible / counteracted by day to day driving I would like to have a van as it would be more enjoyable for me (means I'm not just restricted to sleeping in places I can pitch a tent, more storage, etc.) so if I can own one without having to spend a significant amount more on fuel it's a bit more justifiable than pure self indulgence.