I think the difference is that lomdus relates to questions about the theory of Talmud study or general Talmudic concepts, while halacha-theory relates to questions about theoretical issues about psak and general halacha concepts.
For instance, What is a hakira? and Eating outside of a Sukkah - Lo Tha'aseh or Bittul 'Aseh? are about lomdus and Yerushalmi Versus Bavli in Halacha, Halachic authority of books and What is the meaning of psak? are halacha-theory. Also note that Is the Mitzva of Tzitzit on the Gevra or the Cheftza? is probably both.
I don't gurantee that all the current questions are tagged according to my scheme, but this is how I view it and use it.
EDIT: I think the fact that people don't use the lomdus tag very much is because they are not familiar with the word. Someone should edit in a wiki-summary and maybe we should find a good English word (I don't think "casuistry" is much clearer) to hyphen into the title of the tag.