Conifers do have a tendency to create a fairly large 'dead zone' where the needles fall, and they have a lot of dense surface roots.

As you didn't plant what you have you'd be guessing as to variety and growth habit. They might be tall... Also, if you plan on pruning to maintain size then there is always the risk of bits falling on the cherries while in flower, plus the problem of moving equipment around to actually do the pruning.

Is it possible to use the Thujas as a background to a planting of the cherries rather than an interplanting or are they widely separated?

About the systemic: see what your local agricultural pest control people say. Sometimes a combination of soil and climate can give an unpredictable result. They should have the experience to guide you best.

Yes, a conifer hedge bordering the orchard on the cold and windy sides could assist results by providing shelter. But having mixed the orchard trees and the conifers together could turn out to be a mistake later. An important consideration would be if you will be using machines around the fruit trees, for mowing, spraying etc. The arborvitaes would be likely to get in the way.