PA/DA are based only on the link to the page/domain and don't attempt to distinguish spam from non-spam (except through their dependence on mozTrust, which does do a decent job of identifying spam). As you've noticed, they should be used in combination with some type of spam filter when evaluating sites. There are practical reasons why we cannot or do not want to use PR. One reason is the fact that PR is often out of date as Dr Pete mentioned. Another is that we need to assign a PA/DA to every page and domain in the Mozscape index (>80 billion pages and >150 million domains) and it isn't possible to get PR at this scale.
We have spent some time investigating spam algorithms and I prototyped one last year that I presented at MozCon. We do plan to revisit it in the future, but don't have any immediate plans to do so.
The blog post announcing Just Discovered Links that Keri quoted (