What I mean by “non lmaaseh” are sugyas in shas that most probably will very scarcely be nogeah to our daily life. I understand that to learn these sugyas well will give us a deep understanding of how to think in learning and also take us on a journey to understand the depth of HKBH’s holy Torah. But the bottom line is this: in yeshivas bachrim are encouraged to learn these things and not really pushed to have a set seder in shulchan Aruch , the outcome of this are bachrim knowing some sugyas well but at the same time violating shabbos unknowingly! Is there some reason for how we can allow such a thing and why minhag Yisroel has become to learn this way? (Specifically looking for mekoros from rishonim / early mid achronim whom agree with such an approach to this learning)
The Shulchan Aruch Harav in Hilchos Talmud Torah, and the Iglei Tal in his hakdamah, write that now that the main books have been written, the purpose of yeshiva is to teach students how to understand them.
So it makes sense that yeshivos pick topics that are the most challenging to study, with the idea of "If you can make it here, you can make it anywhere."
That being said, the high schools I know also have time set aside to learn practical halacha from Mishnah Berurah. In post high-school yeshivos, students are expected to make their own time to learn practical halacha from a sefer of their choosing, because they are expected to no longer need guidance to understand practical halacha sefarim.
Eventually (ususally in Kollel), those who want to become rabbanim stop learning just Gemara and start to learn halacha b'iyun, using the Gemara skills they got when they were younger.