A few thoughts. Horticulture involves more intimacy with plants and biotic
communities than agriculture. Perennials, as indidivuals, are with us
longer than annuals. Intimacy and length of exposure would seem to
contribute to the liklihood that one would attribute spirit to something.
Perhaps this is obvious?
The greater complexity of polycultures compared with monocultures may play
a part as well. Complex structure and behavior may draw our spiritual
attention more than simplicity because life is complex and people often
attribute spirit to life. Most spiritual/religious people attribute spirit
to humans. Many to animals. Fewer to plants and other lifeforms. Fewer to
stones and puddles. This is my impression anyway.
My personal understanding of spirit is that it is equivalent to pattern
(rather than energy)--spatial, temporal, structural, functional.
Permaculture involves attention to pattern (spirit) in the system at hand.