The Ionics tank, pump and controller aren't worth anything from a commercial point of view.
IMHO 3k is rather high for the van as a buyer, although the lower mileage would be seen as a positive especially for the seller.
Have a look on ebay to see what similar vans are fetching, but you will need to exclude the pot smoking sellers.
I see someone is trying to get £2195 for a 2008 with just over twice the mileage. Someone else is asking £1495 for a 2005 with 97k on the clock, which would seem about right to me from a retail seller.
I would say that provided it is in mint condition with a full decent service history, it would be valued at around 2k for a private sale as a buyer.
It would be worth less as a trade-in, probably around £1500, unless the garage had a good profit margin across the vehicle he was selling.
Remember, it is 8 years old and having a low annual mileage doesn't mean that it will be a reliable vehicle.