If you were to write an API that is called from Lua (which is 1-based, e.g. table indices start at 1), would you apply the same rule to your API?
For example, say your API had a function called GetFoo(x, y) which returned a Foo at the coordinate (x,y). Would you start your coordinate axes at (0,0) or (1,1) for the API, assuming that in the system itself (say written in C or C++ which are 0-based) these things start at (0,0) (so if you used the Lua convention you would always have to subtract 1 when retrieving numbers for these kinds of operations from the lua stack).
I haven't used Lua, but I would say for a coordinate system specifically (0,0) would be preferred.
For everything else, as long as you state it clearly in the documentation, by all means start indices at 1.