I don't know, I'm afraid. As I understand it, the base ten positional numbering system we use in most of the world (as in, the value of each individual digit is multiplied by ten a number of times based on its position in the number) originated in northern India, but the writing of the people that developed it did not use a lot of punctuation. The modern comma comes from Europe and I'm fairly sure that the idea of a thousands separator comes from Europeans trying to write big numbers in Roman numerals. Based on that I would assume that the British colonial period introduced the idea of using a comma as a thousands separator to India. However, while Europeans were used to thinking in thousands and millions, Indians were habitually thinking in lakhs and crores, so I assume they adjusted the commas to suit that. Since the separators are literally only there to make it easier to read and do not affect any of the maths you can do with it, I don't imagine Indians would have much reason to change their system

Depending on handwriting or font, commas may be more visible than spaces.