I think they are about the same, box or not box. I personally prefer them without a box because I am not a box collector, and I have half a mind to actually throw the packaging away. ... I won't... but I don't like the boxes taking up precious space.
So yeah, I'll spend the same amount on a not boxed pony, if given the chance to offer a price.
BTW, many of the boxed ones over the last year or so went for around $3,000-- at least 3 of them did.
* But it depends on who is looking, what audience is being sold to, and how well it's advertised, and if the person is taking offers.