Could be that what we're shown is just a particularly quiet time for the store, rather than the revival having had no lasting effect. That is, maybe the author is thinking that the bookstore is doing better, but failing to actually show it all that much due to not wanting to crowd the Eizouken folks when they go there - and not having the time to show it at other times due to the need to focus on our lovely cast of goobers.
Or maybe whatever Doumeki is doing will be what revives the bookstore, also Eizouken having 2 models, they can do even wilder promotional stunts now, so i am not too worried about the bookstore
Or maybe they will remake the clocktower with a new script being written by Sakurada, there are so many options really