Nope, the Gojūon (kana table) translates literally as "fifty sounds" because there's the ten consonants times the five vowels.
Five of those combinations don't exist, there's the stand-alone 'n' and two voicing markers for a total of:
50 - 5 + 1 + 2 = 45 + 3 = 48.
So, less than fifty. (There's two forms: hiragana and katakana, but that's kind of like upper and lower case, so I'm not counting that.)
you have the problem of terminal consonants,
Granted; though the Japanese pronunciation is a very soft/nonexistant vowel-sound on -u ends. So "desu" would be pronounced 'des'.
you don’t get away with not having digraphs
True, but there aren't any surprises in the digraphs. (ex: no p + h —> f or t + h —> th [rather than t'hu].)
It was originally fifty symbols, until certain of them were rendered obsolete (in hiragana, “yi”, “ye” and “wu”; a few more in katakana). And we still have some lenition changes (where hiragana “ha” turns into “wa” when used as a particle; “wo” being pronounced “o”). The dakuten and handakuten diacritics expand the sounds.
When it comes to katakana and the Ainu language, they have those small terminal kana that represent terminal consonants. I’ve also toyed with the idea of using dakuten and handakuten with katakana in certain cases to represent non-Japanese vocal sounds (e.g. a dakuten with “ra” to more closely be pronounced like English or Chinese “la”).