I do not know what you exactly mean by territorial economy. If you mean that you look for spatial effects, than of cause spatial econometrics is the way to go.
http://en.wikipedia.org/wiki/Spatial_econometrics
Of cause you need data which cover a spatial dimension to do this, but than you go ahead and do it.
My knowledge of econometrics is that it is statistics and economics used in measurement and they are applicable in many areas where data is concerned and there is need to understand the relationship with the variables so I'm hesitant to agree with you that econometrics is not applicable, unless you clarify your question.
Econometric analysis is useful in Territorial, regional, sub-regional, national, provincial, district, state, or cluster research. You only need to use the right data that reflect the intended scope of the study.