I use PEAR for non-Zen Cart work and like it greatly. It offers a helpful, high-quality repository of code to perform common (and often rather boring) tasks that can greatly reduce development time. However I wouldn't recommend it for Zen Cart.

As I understand it, one of Zen Cart's objectives is to be as widely useable as possible. If it were based on PEAR then that would require that users web hosts had PEAR installed. Although this is likely for Linux servers, it may not necessarily be the case for servers running on Windows. And even users on Linux servers may find themselves having to add specific PEAR modules to their environments (where their hosts allow them).

Instead Zen Cart is almost self-contained, and the external requirements seem to be near universal on decent hosting packages. Furthermore, the core functions that might otherwise be provided by PEAR are under the development team's control, thus avoiding the problems that can occur when a package is developed and tested with one set of PEAR modules, but then run by users whose servers are home to a much wider range of versions.