The entire Cat civilisation rose and fell while Lister was in stasis. Has it been said how much interaction Holly had with them? Did he ever speak to them or were they all based in areas he didn't supervise?
It's hard to prove a negative, but I'd posit that Holly and the Cats didn't interact at all, and that Holly only watched the Cats a little at most.
In the first episode "The End", Holly tells Lister and Rimmer that the Cat is an evolved cat descended from the cat that Lister brought on board all those years ago. This implies that Holly could have watched the Cats at least a little. Holly doesn't seem to know much more than this, though, and we don't find out any more information until the later episode "Waiting for God", in which Holly translates one of the holy books of the Cats for Lister.
It's possible that Holly did interact with the Cats and has forgotten — he's been online for three million years, after all, and is not in the best state. It's also possible that Holly didn't volunteer information because Lister and Rimmer didn't ask.
On balance, though, I don't see that there is any evidence for interaction between the Cats and Holly. At most, Holly watched them occasionally, but not in any great detail.