With regard to Sh'kalim, I believe the answer does indeed rely on publication practices. The practice of printing (and therefore studying) Sh'kalim with the rest of Talmud Bavli Seder Moed can be traced as far back as the times of the Geonim. [The idea is that Sh'kalim is short and therefore relatively inexpensive to print with the rest of Seder Moed to complete the entire seder, compared to something like completing Seder Zera'im with the Yerushalmi. (See here.)] Thus, the inclusion of Sh'kalim in the Daf Yomi cycle is simply a continuation of long-standing tradition of its study together with the rest of Talmud Bavli.
Tractates Midos and Kinim, though, are a separate issue. Why the completion of Seder Kodshim with mishnayos but not the other sedarim? The answer I've always heard given (as well as is speculated here) is that we attempt to finish Seder Kodshim based on the statement of the gemara in Menachos (110a): "When Talmidei Chachamim study the laws of the Temple service, it is considered as though the Beis HaMikdash was rebuilt in their days."