Does Neil read the comments?
No. He occasionally checks the feed to make sure it's working, or if people complain that it's not, but he does not usually read the comments.
How can I ask him a question or make a comment?
On the official Neil Gaiman FAQ page, right underneath the table of contents, is a "Submit a Question" box. If you see a blog entry, you've scrolled too far down.
If Neil doesn't keep an LJ, why is his writing on LJ?
officialgaimain is what's called an RSS feed. Neil's blog has a feed coming from it that LiveJournal picks up and translates into an entry.
More information on LiveJournal and feeds can be found on LiveJournal's syndication FAQ. You may need to poke around a bit, some of the information pages are a little hidden.
Additional questions can be directed to Inuki@ctyalcove.org or posted as a comment on the officialgaiman feed.
This FAQ is maintained by Inuki, and currently hosted by Rochester Institute of Technology, because they have no say in what I use my space for.