I've tested this now and if multiple different size missiles are fired at the same speed each size of missile constitutes a missile salvo. The effect is as I thought, the defending ship can only target one of the missile sizes making point defense much less effective.
Different types of missiles but of the same size are grouped together if they are all traveling at the same speed. This allows them all to be targeted unlike in the case they are different sizes. Presumably, if the missile types have very slightly different speeds, so that they become different salvos but still reach the target in the same 5 second interval, it may also make point defense only able to target one of the missiles, but I haven't tried this.