Im seeing alot of overlap in the use of the two tags and am wondering if there is a functional difference between the two for the site.
There is a potentially useful distinction here: "applied-econometrics" can cover specific questions on implementing models with data, issues with software use (not programming), or also discussion/request of specific applied econometrics studies.
Then, "econometrics" could stand for the more general theoretical questions about properties of estimators, theoretical models etc.
It will be up to users to be careful enough to actually respect and apply this distinction -so if one searches the questions and finds that they don't, it would be an argument in favor of merging/synonymize them.
On the other hand, these are indeed two distinct worlds in econometrics, and in academia the difference is well understood, so perhaps we should keep them distinct in any case.
I have just wrote a short tag-wiki for "applied econometrics" in an attempt to help the situation.