Lua's 1-based indexing is largely inspired by Fortran. Lua's first users were Brazilian engineers in the early 90s, who were mostly experienced in Fortran.

Arguably, one-based indexing is more closed aligned to mathematics tradition. That point about being easier to index the last element helps to iterate backwards over an array. With zero-based indexing, a backwards loop becomes for(i=N-1; i>=0; i--). Yuck.