I think unique buildings or units don't need to be specifically from the civilisation in the game, but can be a shared building that became a unique part of that civs culture and history. You can't separate haciendas from Colombian history, even if they're also part of Mexican and Argentinian history. Missions where uniquely used by the Spanish, but they were also established by the French in New France and the Portuguese and were invented by the wider Catholic Church to spread their religion, not specifically by the Spanish. Many countries have film studios, even France before or at the same time as the USA, but no one can deny that American Hollywood films where a unique cultural phenomenon in the 20th century. And the examples in game could go on and on. That's why I think that such "unique buildings" in-game are justified, even if they're shared historically with other nations.
Though I can see the Lancero used as an unique encampment for a Colombia Civ which also includes modern times, I think it would work better as a unique unit. Maybe as a unique building it could be something like "Lancero Academy" and just "Lancero" as a unique unit. (Fun fact: the Lanceros are actually based, at least in name, on the Llaneros who fought with lances during the independence war).
Even though Haciendas are more of a general Spanish-American building, they do form a huge part of the culture of Colombia, various districts and neighbourhoods in Bogotá (where I live) are actually named after and cover the same territories as former haciendas, conserving the colonial building on the middle. Haciendas were also quite common in Colombia and are heavily regarded as something that's part of the landscape and culture of rural regions and they even became the foundational spot of larger towns and even cities in the 19th century. Moreover, haciendas had variations throughout Latin America and, even though the concept and the name was the same, Mexican, Colombian and Argentinian haciendas have differences that make them stand out, such as architectural features and the type of labour and products they produced. Mexican haciendas are more colourful, while Colombian haciendas are a bit more similar to some Andalusian houses and towns, especially around cities such as Granada and Còrdoba.
However, if there had to be a unique building that's more specific to (Gran) Colombia, I would say that the best choice would be something related to coffee production and the expansion the country had because of this.
It could be a Fonda, or Fonda Paisa, which was like a border outpost or place where settlers from the interior of the country could rest, gather and store resources during the colonisation of parts of the country that hadn't been settled in the 19th century, after the independence. This Fondas where used to colonise the areas that could be suitable for coffee production and would form the basis of coffee haciendas, towns and major cities which formed around coffee production decades after the Spanish had left and in areas that had not been colonised by them before. Even traditional music and songs from the late 19th century revolved around some of these places.
Though the word fonda exists also throughout Spanish-America, meaning just a tavern, in Colombia they became outpost that extended the settlement of the nation into lands unknown to the Spanish in search for suitable land for coffee production as well as other resources, forming a particular cultural identity around it, especially in regions such as Medellín. It can be an unique improvement that extracts resources that are far away from cities and somehow produce culture, gold or could eventually become a normal city.
Another unique building could be Plaza de Bolívar, which is the main square in Bogotá where the Congress, Cathedral, Supreme Court and Townhall are located, all surrounding a statue of Simón Bolívar. Various cities and towns around Colombia and Venezuela (Such as Caracas, Cartagena, Medellín, etc) began copying this in the 19th century and made their own central squares in the cities, also with a statue of Simón Bolívar in the middle and important buildings around it. It could work as a unique monument or as a unique government district that increases loyalty or that generates culture or something, I don't know.
Anyway, sorry for the long post. Even though haciendas aren't only from (Gran) Colombia, they did form a huge part of their culture, so I wouldn't be opposed to having them as their unique building. It did, in part, generate in the country in colonial times as it did in the rest of Spanish America and is a shared heritage with other Latin American influenced areas, all the way up from California to Argentina and, as of now, Gran Colombia in the game seem to attempt to represent or appeal to Spanish America as a whole, so the hacienda still is appropriate.
