Here the "e" doesn't refer to "sìde" (although I think it would also be fine to say "tha i fuar" meaning "it [the weather] is cold"), it's just an abstract point of reference. The choice of gender seems to be quite arbitrary; in Gaelic the masculine form happens to be used (in Ireland we also say "tá sé fuar", and our word for "weather", "aimsir", is also feminine), but in Welsh the feminine form is used: "mae hi'n oer", literally "she is cold", even though "tywydd" = "weather" is masculine. The same "e" also appears in other phrases not referring to the weather, e.g. "Tha e lethuair an deidh a naoi" = "It's half past nine"; "Tha e an urra riut fhèin" = "It's up to you", etc. Whatever the English "it" refers to in such phrases, the Gaelic "e" refers to the same thing.