The cluster of this sibilant with the velar stop is treated in several Indian traditions as though it were a letter in its own right. It is recited at the end of the alphabet after the last consonant, it appears on alphabet charts as a separate item, and children learning to write are taught it as a unit rather than as an assembly of two signs. The reason is partly that its written form in several of the descendant scripts fused into a ligature in which neither component can be made out, and partly that its pronunciation drifted so far from its spelling in the later languages that the connection to its parts stopped being audible.
That is the most conspicuous case of a general phenomenon. A conjunct is in principle a mechanical combination of two letters, and in practice a frequent one becomes a shape learned as a whole, drifts away from its components, and can end up functioning as an additional letter. Brahmi itself keeps the two parts of this cluster visible, which is one of several places where the parent script is more transparent than its children.
It is also why the alphabets of South Asia are quoted with different totals in different books. Whether this cluster counts, and whether the anusvara and visarga count, decides whether the traditional figure comes out at forty-six, forty-eight, forty-nine or fifty.