I think that there are several layers to it.
First, as mentioned several times throughout the series, Z-space can shift, and can make a journey take more or less time.
Another, and I personally think more likely is that the Andalites kind of don't care. They figure that they can do the same thing to Earth that they did to the Hork-Bajir planet, release a virus and wipe out the hosts.
As far as responding to Aldrea and not Ax, the incident with Aldrea on the Hork-Bajir planet was the first major attack by the Yeerks on a species, hence their response to prevent it. After the Yeerks conquered the Hork-Bajir, as you pointed out, they are warring across the galaxy against Yeerks who are now far reaching due to their Hork-Bajir and after that Taxxon hosts. As we know, there was quite an open war on Leera, and there were a lot of troops from both sides there. Perhaps the Andalites thought that since the invasion of Earth was being done slowly, in secret, they thought they had more time.
Those are my thoughts on it anyways.