No they're definately 4" in Bose or non-Bose. In fact all the speakers are 4" on the Bose system.
They can be upgraded, but the benefit is minimal if anything on the Bose system. The Bose speakers are 2 ohm impedance as well, so either need 2 ohm replacements or can be 4 ohm but will need the Bose amp to be driven a bit harder. If you want better sound then fit a sub, fannying around with just the speakers does very little and are a pain to fit as you need adapter rings and have limited depth (about 60mm including the spacer rings).