It means that when you ordered your site, you made it easier for xenforo to sequence your site's structure. For example, suppose your first forum [display-wise] is Announcements, the ID number for that forum is 1, if your introduction forum is the second one, its #2. Get it?
It does not matter what ID number your announcement or introduction forum is. The way that YOU structured your forums will be indexed in THAT order.
Besides which-ever url structure you use, it is indexed regardless. There's a SEO switch in the xenACP.
Importing from vb3.x is built-in, so yes, your vb3.8.x would work.
Those "missing" numbers will be depreciated. Whatever you have visible will be structured by xenforo from 1 through [insert number here]. Although this will cause a mis-index by search engines, it should not affect your site's SEO, or indexing. In fact, it will have a better effect on your site. A lot of the VB-powered sites have beem imported and reported astronomical numbers.
It might make 1 become 2, but don't really expect it to go from 1 to 1,xxx,xxx,xxx, where x are actual numbers. That said, XenForo also supports URL redirection from your vBulletin forum to your XenForo one so you don't really need to worry about it anyways.