1) vBulletin's templates are extremely flexible, at least in comparison to Ultimate Bulletin Board and phpBB, in which I've used in the past. A major factor is that they are separate from the core vB PHP files and so when you upgrade it will not affect your custom template configurations, unless it's a major change to routines. In such cases you will manually change them back to default and can re-customize them again to meet the upgraded version requirements. The templates are stored in the database so there are no files to edit.
While vB uses Tables for its layout you can customize it to use CSS. Not only have I've seen vB forums do it but I've experimented too and it can be achieved, but with work as there are a lot of default templates to go through (quite overwhelming in the beginning). One day I'll showcase (and possibly release) a fully compliant XHTML and CSS design.
2) vB.org has a ton of talented coders/designers that may be able to help you. Depending on the modification a fee may be required. You can request "hire for help" in the Services forum.
The coders are very good at developing mods that do not conflict with others that are installed. Then there are mods that integrate with other mods. Your templates should remain intact. My guess is that if a mod requires a certain style layout (e.g., CSS pure) then work with the coder/designer during the process.
3) vBulletin uses ajax and so do many of the mods here. So I'd say 'yes' to your question.
I'm fairly new to vB as well so I'm sharing my experiences. I hope it helps.