that's a whole different problem, though. your first problem was whether japanese would have some sort of new or unique problem with an alphabet given the absence of certain syllables (like shi) from the language. the answer is, of course, no: the language would fall into either of the two extant conventions for dealing with the syllable: always write "shi", or write "si" and just change the pronunciation.
no written language stands independent of its pronunciation rules. alphabets need a somewhat larger set of rules than syllabaries, but that's true independent of language.
