It gets worse. Imagine you'd like to try to look for possible suffixes corresponding to "the" as an alternative (I don't know any languages that uses other methods, but I'm sure they exist).
Imagine now if your "unknown" language was similar to Norwegian. In Norwegian "the sun" can be either "solen" or "sola" depending on gender, and you can't assume a writer is even consistent (it's bad form to mix different gender for the same word in the same text, but that doesn't stop people), which would throw off your counts/stats.
We have a pretty good catalogue of possible variations based on modern languages, so you certainly could try to construct a theory of a mapping based on known possible options (and you're not wrong to think in that direction as one approach worth testing), but there are many possible variations, so it's unfortunately not an easy one.
Reading https://en.wikipedia.org/wiki/Article_(grammar)#Tables, Maltese uses prefixes.