A 1 - AFAIK the Spiders used by search engines rely heavily on text content when indexing sites. So I don't think it's the case that they aren't crawled at all. It's more likely that googles spiders/crawlers are unable to see much of the text/infomation contained in flash sites as much of it is embedded in .swf files rather than in the HTML files (which is where the spiders concentrate on finding/indexing information). So Flash content always seems to trip them up. However there are ways to improve SEO for flash websites.
There is a good article about SEO and flash websites here:
A 2 - AFAIK, CSS is fine. When used properly CSS can actually aid Search engines / SEO. There are a few CSS techniques that can affect your ranking in a negative manner, but generally speaking using CSS is a good thing!
Take a look at this article: