doubleThow can he be a mummy in the first place, the Incas didn't embalm their dead.
They didn't use voodoo dolls or operate telepathic control over victims, or have people sneak around with crystal balls full of a mysterious substance either, for that matter... Hergé was just being fanciful with his material.
But they did
(according to at least this National Geographic
article) have mummification.
As it happens, the mummy of "Rascar Capac" is based on a real artifact as Tintin Quiz's reference says - see here
for an image of the actual Peruvian mummy in a mock-up of the library at the museum in Brussels during an exhibition.Update:
I just realised that I slightly misinterpreted your remarks, and did not address as to why naturally preserved mummies would be in a structure. Well, I suppose that the cave in which the mummies are found (as seen on the cover, as opposed to Rascar Capac) might be a structure, but it seems perfectly possible that once the mummification had taken place by wind and sun (assuming the bodies were mummified by exposure), that there would be a point at which they would be moved to an ossuary or similar for veneration or storage, as it were.
Remember that the bound mummies, as seen on the cover, were based firmly on illustrations in a book of Peruvian exploration, Pérou et Bolivie
(1880), by Charles Wiener (the mask is illustrated on p.649, for example).
So authentic was Hergé's work that, apparently, a government official refused to believe that he had not visited the country and done his work first hand, and checked the records of immigration to prove that Hergé had been there (he hadn't...).