That pogrom was in 1906 so it can't have made people living a century earlier hide their ethnicity.
Great-Granddad was born in 1904, when the Faber-Kogan incident happened. The incident became the catalyst for the Anti Semites to find another excuse for a pogrom, this time the Belostok Pogrom. Great-Great-Grandma and Great-Granddad could not leave until 1908. By the way, the Anti Semitism began to be really bad in 1795 under Catherine the Great, and a census in 1787 (eight years before the First Partition, which came 20 years before the Conference of Vienna) has a really-interesting comment for one of Great-Great-Grandma's paternal relatives in Kuty, Ukraine: "Żyd". I doubt that it was meant to be just descriptive:
Kopel ANDRULOWICZ
Property record
1787
Year:1787
Town:Kuty
House Number:208
Topographic number:283
Comments:Jew (Żyd)
To pawian as well, I have tried almost everything and am now also reaching out to Genekta and Genealodzj.PL as well. Also, Ruchla (as the manifest actually reads, I realized upon more closely reading the manifest) gave "Wilna" and "Wilne", not "Vilna" and "Vilne". So, she gave the Polish transliterations of the Russian and Yiddish names. I will also look at the sources that you provided, though.