If voting "yes" on a referendum to be annexed is an accurate way of knowing that the majority of the populace supports annexation, does the same logic apply to Crimea being annexed by Russia? If not, why not?

The choice was to become a state or remain a territory. Either yes or no would have had Hawaiian peoples occupied. Statehood could be seen as a regaining a scrap of self determination but all it ended up doing was impoverishing the natives and ceding all wealth to colonizing capitalists. This is a primarily function of bourgeois democracy.

Should I kill you with my sword or with my gun?

Sorry, "I want to live" was not an option on the ballot

from your own link

In 1897, over 21,000 Natives, representing the overwhelming majority of adult Hawaiians, signed anti-annexation petitions in one of the first examples of protest against the overthrow of Queen Liliʻuokalaniʻs government.[143] Nearly 100 years later, in 1993, 17,000 Hawaiians marched to demand access and control over Hawaiian trust lands and as part of the modern Hawaiian sovereignty movement.[144] Hawaiian trust land ownership and use is still widely contested as a consequence of annexation. According to scholar Winona LaDuke, as of 2015, 95% of Hawaiʻiʻs land was owned or controlled by just 82 landholders, including over 50% by federal and state governments, as well as the established sugar and pineapple companies.[144] The Thirty Meter Telescope is planned to be built on Hawaiian trust land, but has faced resistance as the project interferes with Kanaka indigeneity.[clarify][145]

If you think a referendum from 1959 fairly represents the interests of the native population then what else is there to say.

https://en.m.wikipedia.org/wiki/Overthrow_of_the_Hawaiian_Kingdom

note the dates. it was forcibly annexed by a coup government. the later vote to join as a state took place well afterwards