I dunno - in some of the earliest (pre-Barnabas) episodes, Liz does not take well to Vicki's constant questioning; she gets pretty hostile with her on a couple occasions, and even threatens to fire her. Of course, that might happen with a long lost daughter, maybe Liz was trying hard to overcompensate so that no one would guess her secret? While it's clear in the early storylines that Elizabeth knows something about Victoria's background, and isn't willing to tell anyone (including Roger) what she knows, have to say I'm among those who find those early episodes to have a very ambivalent feel both in terms of writing and acting about the true parentage of Victoria Winters. A little later on, particularly after the 1795 storyline, I agree that Joan played Liz very much as if she was Vicki's mother.
The character of Elizabeth Collins Stoddard is endlessly fascinating to me. She seems to be an illustration of that old adage "still waters run deep." Seems like there is always another layer with the woman, as if you can never really know her. Joan Bennett was really terrific in playing this character, but then she was good with all her DS characters.