Here is an example of the process to apply redactions to a PDF file (or any sort of electronic document). The document is opened in a third-party native viewer with redaction capabilities (and not in the original application like Arcobat or Office). The end-user draws a black box over the appropriate text using the third-party native viewer. This redaction is saved as a separate layer that can be rendered on top of the native document when viewed in the software, as well as printed out. Finally, when documents need to be produced for court, they are printed out to a TIFF-printer driver, effectively converting them to TIFF and "burning in" the redaction layer. The TIFFs are delivered to the courts and opposing council.
The pre-processing is largely automated but there's certainly a portion (maybe 5%?) of documents that need to be hand-classified in the database before they get to the lawyers. It an interesting field - lots of money to be made, intense competition for it, relatively simple technology requirements but a legal industry which has been resistant to technology for quite a long time. Autonomy seems to be the leading software company in this space.
I suppose the (extremely limited) redaction features in Acrobat stem from the belief that the document is ultimately destined for printing rather than computer reading.