Sorry I didn't respond sooner. I think I found an easier explanation than Layton's and Shisha-Halvey's.
First of all, I'd like to point out that not every Coptic manuscript has the indefinite article. On the Unboundbible.org, the Bohairic and Sahidic versions taken from J Warren Wells' Sahidica uses the definite article in both dialects. This is strange since Wells comment on the Apologetics site Dzheremi' gave us is exactly what the JW's claim - that the Sahidic version always has the indefinite article and that the Logos was "like" God. (Sounds like Arianism to me. But that's a different subject.)
Second, JW's have failed to recognize that the Coptic "ou", the indefinite article, has multiple usages. Linguistically, (and I hope Dzheremi can confirm or correct what follows), I believe "ou" refers to the partitive article. According to Wikipedia, "A partitive article is a type of indefinite article used with a mass noun such as water, to indicate a non-specific quantity of it...The nearest equivalent in English is "some", although this is considered a determiner and not an article." Other mass nouns include water, light, love, air, wind, spirit and God. Just like in English, if I say "Give me water" (no article), I must mean "Give me some water" or more syntactically accurate, "Give me part of the mass noun water". In Coptic, it would be "Ti `noumwou nyi" - (Literally, give me a water.) You must use "ou". You can't use the zero article like Greek. The zero article exists in Coptic, but only with specific prepositions and circumstances that do not apply here. The same is true with 1 John 4:16 "God is love." In one manuscript the Bohairic says "God is a love", the Sahidic says "God is the love". The Greek (I believe uses the definite article). The same is true in the Nicene Creed. The Greek says, "Φῶς ἐκ Φωτός, Θεὸν ἀληθινὸν ἐκ Θεοῦ ἀληθινοῦ," (Light of light, True God of True God). The Coptic uses "ouwouini evol qen ouwouoini. ounouti entaevmi evol khen ounouti entaevmei" To the untrained eye, it could be translated "a light out from a light, a true God out of a true God". Wikipedia's definition of mass noun is "a mass noun (also [called] uncountable noun or non-count noun) is a noun with the syntactic property that any quantity of it is treated as an undifferentiated unit, rather than as something with discrete subsets." It would be completely syntactically wrong to say "a light from a light" since these nouns must be treated as undifferentiated units, not a subset. It is also syntactically wrong to translate John 1:1c as "the Word was a god" in the context given.
JW's have attempted to substantiate their heresy by claiming a conspiracy of hiding the Coptic version. They insist John 1:1c should be read as a common indefinite article and fail to realize that the text uses the partitive article. This reinstates Layton's comment "Don't worry about the indefinite article of John 1.1 in Coptic; it might mean was a god, was divine, was an instance of 'god', was one god (not two, three, etc.). The range of meanings of the Coptic indef. article does not map nicely onto English usage, nor Greek. Once you learn Coptic you will know all of this."
Severian, my answer your last question is no. The fact that there are some versions of Coptic bible with the definite article probably means that some Coptic translators were not concerned about Sabellianism, but rather understood the Trinitarian formula that the Word was (the) God. I think the use of the indefinite article in some manuscripts has to do with a proper recognition of no article in Greek and the various grammatical uses of the indefinite article in Coptic, not found in Greek. It really has nothing to do with theology but JW's made it theological.
Does this help?