My belief is that they were three nameless Pokemon (I'd say 3 of the same species, and a species we probably have never encountered before as they're said to be "nameless") As coolcatkim22, I think Ho-Oh resurrected them into Legendary Beasts based on the three main elements that related to the Tower's downfall. The three beasts also resembling dogs, and it's widely accepted that dogs are brave and caring animals; they might have been killed while they were helping other Pokemon out of the building, ultimately sacrificing themselves. Ho-Oh saw Entei, Raikou and Suicune as the appropriate forms to bring these dead Pokemon back into (as Bulbapedia mentions, it's believed that these three legendary dogs are not the only ones of their species. Meaning of course that there are more than one of them.)
Lots of possibilities of course and the Eevee evolution trio makes sense, but for some reason I can't see that as being the appropriate answer.