The reason why "llama" is spelled with two "l's" is because the word was borrowed directly from Spanish, where the double "ll" is a distinct letter and digraph. In Spanish, the "ll" is typically pronounced like the English "y" as in "yard." English adopted the spelling from Spanish but pronounced the double "l" simply as a single "l" sound. The word "llama" comes from the Quechua language via Spanish and refers to the South American domesticated mammal. This spelling preserves the original Spanish form even though the English pronunciation does not replicate the Spanish "ll" sound.
Additionally, the double "l" is quite common in Spanish and other languages, though it is rare as the starting letter in English words. The spelling "llama" distinguishes this specific animal and reflects the etymological history of borrowing from Spanish.