The article describes a bad programmer as one whose programs “die young”. I would guess that Knuth is saying is that the longest one of his programs lived (was used?) for 12 years?

If that is what he meant, I presume this remark was written well in the past, as TeX has lasted way more than 12 years.

The note is actually from Chuck Baker, the editor of that issue of Datamation.

You're not alone in assuming DEK wrote the note, a lot of people seem to attribute it to Knuth.