Forty-seven letters do not account for everything written in Siddham. A set of marks sits alongside them, none of which is counted among the letters and all of which are needed to write the language. Two are sounds in their own right. The nasal mark, written above the syllable, indicates a nasal quality carried by the vowel; the mark written after it, a pair of dots, indicates a breath released at the end of a word. Both appear constantly, and both are essential to the seed syllables of East Asian esoteric Buddhism, where a great many of the syllables are a letter plus one of these marks rather than a bare letter.
A third mark does the opposite job. It cancels the vowel that a consonant sign automatically carries, so that the consonant can close a syllable with nothing after it. Without it an abugida cannot write a word ending in a consonant at all, and Sanskrit has a great many.
The distinction between letters and marks matters for anything that counts. A reference work listing the Siddham characters may be counting the letters of the traditional order, or the letters plus the dependent vowel signs, or everything an encoding needs in order to reproduce a manuscript. The three numbers are different and each is right for its question. What the tradition itself names as the syllabary is the forty-seven.