If I cast a "muffle" spell, will that also cause Lydia, my housecarl, to move quietly? Or is there really no point in casting muffle is Lydia is with me?
Thanks

No it will not, it isn't area of effect, it will only affect you.

You can use a muffle enchant (the same at any enchanting level) to muffle her boots, then she won't cause you sneak problems.