There are actually three characters that are pronounced the same as three other characters, but those are entered in different ways for structural reasons, and Japanese characters are neatly arranged on a grid in a way that is sensible that does not necessarily correspond to pronunciation well but corresponds well to structure. The character entered with <ti> for instance in pronunciation corresponds more closely to the digraph entered with <tya>, but in structure corresponds more closely to the character entered with <ta>, and is therefore found on the same row.
When all digraphs and characters are summed's close to 90 characters I believe, which does not fit neatly on a keyboard, and then even enter the modern digraphs that are used in loan transcription which do not correspond to any native structure of Japanese which probably add another 20-30 characters which are also made with structural combinations that make sense. <thi> is a common combination to enter something that has nothing to do with the pronunciation <th> would suggest, but it structurally makes sense.
And then on top of that there are various nonsense accents and other modifications that officially have no place in the standard language but find their way in creative language.
If English had 80 characters in it's script, but the characters so neatly corresponded in a structural way that they could be arranged nicely on a grid, typing methods would probably also rely on combining simpler forms to produce them rather than have a keyboard that spans the full range as it's simply more efficient.