1) I include below what the Kollel wrote about your question in our Introduction to Masehches Shekalim

2) Shekalim was included in the first cycles. See below for a copy of what we wrote about the history of the Dafyomi cycle and Shekalim, also taken from our Introduction to Maseches Shekalim.

Best wishes,

Mordecai Kornfeld

Kollel Iyun Hadaf

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From Introduction to Maseches Shekalim

(b) Maseches Shekalim is unique in that it is the only Maseches of the Yerushalmi that is printed in the common editions of the Shas Bavli, and is included in the Dafyomi cycle. The obvious question is, why? Although the Mishnayos of those Masechtos for which Gemara was not written were traditionally included in the Shas, it is puzzling why the entire Gemara Yerushalmi was included in this instance, as opposed to the Yerushalmi on Zera'im. Perhaps it was included since it is the only Maseches in Moed for which a Gemara Bavli was not written, whereas no Bavli was composed for nearly the entire Zera'im. Since it meant only a few extra pages, the otherwise frugal printers decided in the case of Shekalim to include the full Yerushalmi and not just the Mishnayos. (For unknown reasons, Yerushalmi Horayos is also included in some printings of the Shas Bavli, perhaps due to the brevity of the Bavli on that Maseches.)

A harder question to answer is why the founder of the Dafyomi cycle, Rav Meir Shapiro, zt'l, included it in the cycle. His intention may have been to complete Seder Moed -- a hypothesis confirmed by the fact that he included Mishnayos Kinim and Midos in the cycle to complete Seder Kodshim -- but then why did he not include Mishnayos Eduyos to complete Seder Nezikim? (Avos was understandably left out because it is learned in either case, between Pesach and Sukkos.) Perhaps this Maseches, and Kinim and Midos as well, were included in order to fulfill the teaching of Chazal that "When Talmidei Chachamim study the laws of the Temple service, it is considered as though the Beis ha'Mikdash was rebuilt in their days" (Menachos 110a).

(c) There is no standard Daf-length in the Yerushalmi; rather, the length of the Daf is determined by the commentaries that happen to be printed alongside it. Since each printing of the Yerushalmi includes different commentaries, each has a different number of Dafim per Maseches. For example, Shekalim as printed in the Vilna Shas (Bavli) goes until Daf 22, in the Warsaw Shas until Daf 30, in the Zhitomir Shas until Daf 13, and in the original printing (Venice 1522, with only the Rambam's Perush ha'Mishnah) only until Daf 12. The length of Shekalim in editions of the Yerushalmi vary in length as well; it goes until Daf 33 in the Vilna Yerushalmi, while in the Zhitomir Yerushalmi it only reaches Daf 31. Incidentally, this phenomenon explains the mysterious "lengthening" of the Dafyomi cycle in the eighth Dafyomi cycle (which began in June 1975). Rav Meir Shapiro's original calendar was tailored to a 13 Daf Shekalim. When that edition became uncommon, the cycle was changed to accommodate the 22 Daf version of the Vilna edition, lengthening the Dafyomi cycle from 2702 days to 2711 days.