I think the 'ku' is the past tense infix, while the 'ku' of 'kuwa' is dropped because it is a monosyllabic verb root. E.g. 'nilikula' becomes 'sikula' in the past test. If someone knows better please correct me. It seems we have to avoid saying 'kuku' in the middle of a word, because that would be chicken.
That's not truth, ku- exists - " ku" - wa ( kuwa ). In PROPER construction of "- li -" past tense negation we have : si / h ( ha for plural) + person + ku + thema of verb. Kitabu is a thing and it's prefix is " ki". And "a" is given for better pronounsing. So, we have as result - h(a) + prefix " ki" + ku + thema of verb " wa" ( from kuwa ) - hakikuwa. By the way - is it maybe " kuwa" a monosyllabic or irregular verb ?