Where there always plans for there to be multiple Makuta or was it though of later. If so, when?
I'm 98% sure that there wasn't. Mainly due to the fact teridax is referenced as "the makuta" or "makuta", and how there is never a mention of many makuta making rahi just one, and finally he is said to be mata nui's brother.
The first time Makuta alludes to other members of his kind is in Legends of Metru Nui, where he invites Vakama to join him and his brothers. But I also seem to recall Greg saying the idea came about in 2005.
To my knowledge, no, that was not part of the original plan. But I also don't know how far the original plan extended in detail, since no one expected the line to last as long as it did.